When you see in NPS@ the sentence "Paste a multiple protein alignment in clustalw format below", you must paste a clustalw alignment as indicated below.

MULTIPLE PROTEIN ALIGNMENT IN CLUSTALW FORMAT :

CLUSTAL W (1.8) multiple sequence alignment


CCPA_BACME      ----MNVTIYDVAREASVSMATVSRVVNGNP---NVKPSTRKKVLETIERLGYRPNAVAR
CCPA_BACSU      ---MSNITIYDVAREANVSMATVSRVVNGNP---NVKPTTRKKVLEAIERLGYRPNAVAR
CCPA_STRMU      MNTDDTITIYDVAREAGVSMATVSRVVNGNK---NVKENTRKKVLEVIDRLDYRPNAVAR
DEGA_BACSU      ----MKTTIYDVAKAAGVSITTVSRVINNTG---RISDKTRQKVMNVMNEMAYTPNVHAA
FRUR_ECOLI      ------MKLDEIARLAGVSRTTASYVINGKAKQYRVSDKTVEKVMAVVREHNYHPNAVAA
RBTR_KLEAE      ---MKKITIYDLAELSGVSASAVSAILNGNWKKRRISAKLAEKVTRIAEEQGYAINRQAS
                       .: ::*. :.** ::.* ::*..    .:. .  :**     .  *  *  * 

CCPA_BACME      GLASKKTTTVGVIIPDISNIFYAELARGIEDIATMYKYNIILSNSDQNQDKELHLLNNML
CCPA_BACSU      GLASKKTTTVGVIIPDISSIFYSELARGIEDIATMYKYNIILSNSDQNMEKELHLLNTML
CCPA_STRMU      GLASKKTTTVGVVIPNIANAYFSILAKGIDDIATMYKYNIVLASSDEDDDKEVNVINTLF
DEGA_BACSU      ALTGKRTNMIALVAPDISNPFYGELAKSIEERADELGFQMLICSTDYDPKKETKYFSVLK
FRUR_ECOLI      GLRAGRTRSIGLVIPDLENTSYTRIANYLERQARQRGYQLLIACSEDQPDNEMRCIEHLL
RBTR_KLEAE      MLRSKKSHVIGMIIPKYDNRYFGSIAERFEEMARERGLLPIITCTRRRPELEIEAVKAML
                 * . ::  :.:: *.  .  :  :*. ::  *       ::  :    . * . .. : 

CCPA_BACME      GKQVDGIIFMS---GNVTEEHVEELKKSPVPVVLAASIESTNQIPSVTIDYEQAAFDAVQ
CCPA_BACSU      GKQVDGIVFMG---GNITDEHVAEFKRSPVPIVLAASVEEQEETPSVAIDYEQAIYDAVK
CCPA_STRMU      AKQVDGIIFMG---HHLTEKIRAEFSRARTPVVLSGTVDLEHQLPSVNIDHSKAAQDAVA
DEGA_BACSU      QKKVDGIIFATGIESHDSMSALEEIASEQIPIAMISQDKPLLPMDIVVIDDVRGGYEAAK
FRUR_ECOLI      QRQVDAIIVSTS--LPPEHPFYQRWANDPFPIVALDRALDREHFTSVVGADQDDAEMLAE
RBTR_KLEAE      SWQVDWVVATG---ATNPDKISALCQQAGVPTVNLDLPGSLS--PSVISDNYGGAKALTH
                  :** ::                      * .             *           . 

CCPA_BACME      SLIDSGHKNIAFVSGTLEEPINHAKKVKGYKRALTESGLPVRDSYIVEGDYTYDSGIEAV
CCPA_BACSU      LLVDKGHTDIAFVSGPMAEPINRSKKLQGYKRALEEANLPFNEQFVAEGDYTYDSGLEAL
CCPA_STRMU      LLAKH-HDKIAFVSGPLIDDINGKVRLAGYKEGLKKKGLPFKEGLVFEAQYKYQEGYQLA
DEGA_BACSU      HLLSLGHTNIACIIG-DGSTTGEKNRIKGFRQAMEEAGVPIDESLIIQTRFSLESGKEEA
FRUR_ECOLI      ELRKFPAETVLYLGA-LPELSVSFLREQGFRTAWKDD--PREVHFLYANSYEREAAAQLF
RBTR_KLEAE      KILAN--------SARRRGELAPLTFIGGRRATITPAS----V-YAASTMRIASWGLACR
                 :            .             * :                      . .    

CCPA_BACME      EKLLEEDEKPTAIFVGTDEMALGVIHGAQDRGLNVPNDLEIIGFDNTRLSTMVRPQLTSV
CCPA_BACSU      QHLMSLDKKPTAILSATDEMALGIIHAAQDQGLSIPEDLDIIGFDNTRLSLMVRPQLSTV
CCPA_STRMU      QRVINSG--ATAAYVAEDELAAGLLNGLFAAGRKVPEDFEIITSNDSTIALYTRPNMTSI
DEGA_BACSU      GKLLDRN-APTAIFAFNDVLACAAIQAARIRGIKVPDDLSIIGFDNTILAEMAAPPLTTV
FRUR_ECOLI      EKWLETHPMPQALFTTSFALLQGVMDVTLRRDGKLPSDLAIATFGDNELLDFLQCPVLAV
RBTR_KLEAE      RRIFWLP-----------AIRKATLRTACRSG--LAARR--R---------CCRGYLLTR
                 : :               :  . :      .  :.                    : : 

CCPA_BACME      VQPMYDIGAVAMRLLTKYMNKETVDSSIVQLPHRIEFRQSTK----
CCPA_BACSU      VQPTYDIGAVAMRLLTKLMNKEPVEEHIVELPHRIELRKSTKS---
CCPA_STRMU      SQPIYDLGAVAMRMLTKIMNKEELEEKEIVLNHGIKKRGTTK----
DEGA_BACSU      AQPIKEMGAERHRTAGRSNRGKRKAKQKIVLPPELVVRHSTSPLNT
FRUR_ECOLI      AQRHRDVAERVLEIVLASLDEPRKPKPGLTRIKRNLYRRGVLSRS-
RBTR_KLEAE      RYPWKGLCAGCRRWV-------------------------------
                      :     .

ALLOWED CHARACTERS :

ABCDEFGHIKLMNPQRSTUVWXYZ
Warning : Some softwares don't understand some characters. Please, refer to NPS@ help about these sofwares (PFMAKE and HMMBUILD).

CODES :

   A   alanine               B   aspartate or asparagine
   C   cystine               D   aspartate
   E   glutamate             F   phenylalanine
   G   glycine               H   histidine
   I   isoleucine            K   lysine
   L   leucine               M   methionine
   N   asparagine            P   proline
   Q   glutamine             R   arginine
   S   serine                T   threonine	
   U   selenocysteine        V   valine
   W   tryptophan            X   any
   Y   tyrosine              Z   glutamate or glutamine