BLASTP 2.2.18 [Mar-02-2008] Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. Reference for compositional score matrix adjustment: Altschul, Stephen F., John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis, Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109. Query= 0345.0021.p (464 letters) Database: COG 115,334 sequences; 38,378,431 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value alr0991 [P] COG0004 Ammonia permease 315 1e-85 STM0402 [O] COG0450 Peroxiredoxin 313 4e-85 sll0108 [P] COG0004 Ammonia permease 297 2e-80 AF1746 [P] COG0004 Ammonia permease 288 2e-77 MA4207 [P] COG0004 Ammonia permease 249 6e-66 >alr0991 [P] COG0004 Ammonia permease Length = 359 Score = 315 bits (806), Expect = 1e-85, Method: Compositional matrix adjust. Identities = 0/444 (0%), Positives = 0/444 (0%), Gaps = 12/444 (2%) Query: 20 VSAFAADGPTAPDLQIGLDTAFTFLAFILVFFMQAGFAMLEAGSVRMKNAGHVAGKTVLT 79 + + L F + Q + + V Sbjct: 60 LEEALRLRAGGITKPVLLLEGFFDARDLPTISAQHFHTAVHNEEQLAALEEASLDEPVTV 119 Query: 80 LAIASLCFWAIXXXXXXXXXXXXXXXXXXLYGG--------DTQAASFDSLAFSDVTLNV 131 + + + Sbjct: 120 WMKLDTGMHRLGVRPEQAEAFYHRLTQCKNVRQPVNIVSHFARADEPKCGATEKQLAIFN 179 Query: 132 KFLFQMAFAAVSLAIVSGGMAERAKLSVYIVFGILFSVVIYPVVAHWVWGGGWLAELGMQ 191 F A + ++ IL+ V + G Sbjct: 180 TFCEGKPGQRSIAASGGILLWPQSHFDWVRPGIILYGVSPLEDRSTGADFGCQPVMSLTS 239 Query: 192 DYAGSTVVHLTGATAAVVATILLKPRLGKFNKEGKPVIIPGHNQVFTVLGVIILWFGWFG 251 + + ++ Sbjct: 240 SLIAVREHKAGEPVGYGGTWVSERDTRLGV-VAMGYGDGYPRAAPSGTPVLVNGREVPIV 298 Query: 252 FNPGSALSPMGGFFGHVALTTNXXXXXXXXXXXXXSWLYFGKSDIPAMLNGVLAALVAIT 311 + + + S + + Sbjct: 299 GRVAMDMICVDLGPQAQDKAGDPVILWGEGLPVERIAEMTKVSAYELITRLTSRVAMKYV 358 Query: 312 GACAFVEPWAAILIGFVAGAFTFMTSQWLERAGLDDPIYAFSVHGIAGMWGAVSTGLFAT 371 Sbjct: 359 418 Query: 372 -PDLIT--KGALVGKAGLFYGGGFHQLGVQILGVAGTFVFVAVMSFIILYVMKLVIGLRV 428 Sbjct: 419 478 Query: 429 TEEEELMGLDISEHGTYGYPEQMK 452 Sbjct: 479 502 >STM0402 [O] COG0450 Peroxiredoxin Length = 200 Score = 313 bits (801), Expect = 4e-85, Method: Compositional matrix adjust. Identities = 0/450 (0%), Positives = 0/450 (0%), Gaps = 23/450 (5%) Query: 1 MRKKMIMMFLAMITLMVYPVSAFAADGPTAPDLQIGLDTAFTFLAFILVFFMQAGFAMLE 60 M ++ T + F Sbjct: 1 MVLVTRQAPDFTAAAVL----GSGEIVDK--FNFKQHTNGKTTVLFFWPMDFTFVCPSEL 54 Query: 61 AGSVRMKNAGHVAGKTVLTLAIASLCFWAIXXXXXXXXXXXXXXXXXXLYGGDTQAASFD 120 + G V+ ++ S Sbjct: 55 IAFDKRYEEFQKRGVEVVGVSFDSEFVHNAWRNT--------------PVD--KGGIGPV 98 Query: 121 SLAFSDVTLNVKFLFQMAFAAVSLAIVSGGMAERAKLSVYIVFGILFSVVIYPVVAHWVW 180 A + G A V + + Sbjct: 99 KYAMVADVKREIQKAYGIEHPDEGVALRGSFLIDANGIVRHQVVNDLPLGRNIDEMLRMV 158 Query: 181 GGGWLAELGMQDYAGSTVVHLTGATAAVVATILLKPRLGKFNKEGKPVIIPGHNQVFTVL 240 Sbjct: 159 218 Query: 241 GVIILWFGWFGFNPGSALSPMGGFFGHVALTTNXXXXXXXXXXXXXSWLYFGKSDIPAML 300 Sbjct: 219 278 Query: 301 NGVLAALVAITGACAFVEPWAAILIGFVAGAFTFMTSQWLERA-GLDDPIYAFSVHGIAG 359 Sbjct: 279 338 Query: 360 MWGAVSTGLFATPDLITKGALVGKAGLFYGGGFHQLGVQILGVAGTFVFVAVMSFIILYV 419 Sbjct: 339 398 Query: 420 MKLVIGLRVTEEEELMGLDISEHGTYGYPE 449 Sbjct: 399 428 >sll0108 [P] COG0004 Ammonia permease Length = 507 Score = 297 bits (760), Expect = 2e-80, Method: Compositional matrix adjust. Identities = 180/477 (37%), Positives = 259/477 (54%), Gaps = 35/477 (7%) Query: 1 MRKKMIMMFLAMITLM-----VYPVSAFAAD-----------GPTAPDLQIGLDTAFTFL 44 +R+K+ +LA + L ++ +A A D LQ L+ + + Sbjct: 36 VRRKINSPWLACVPLTALIVAIWNAAAIAQDTEIVNITVETVNENVATLQGTLNAIWILI 95 Query: 45 AFILVFFMQAGFAMLEAGSVRMKNAGHVAGKTVLTLAIASLCFWAIXXXXXXXXXXXXXX 104 A ILV FM AGF MLE G R KNA ++ K ++ A+A++ +WAI Sbjct: 96 AAILVIFMNAGFGMLETGLCRQKNAVNILTKNLIVFALATIAYWAIGFSLMFGSSGNPFV 155 Query: 105 XXXXLY-GGDTQAASFDSLAFSDVTLNVKFLFQMAFAAVSLAIVSGGMAERAKLSVYIVF 163 + GD + + V FLFQ+AF+A + IVSG +AER K + +++F Sbjct: 156 GFGGFFLSGDHTNYGLSPFP-EGLPVAVFFLFQVAFSATAATIVSGAVAERIKFNEFLIF 214 Query: 164 GILFSVVIYPVVAHWVW-GGGWLAELGMQDYAGSTVVHLTGATAAVVATILLKPRLGKFN 222 +L + YP+ HWVW GGWL +G D+AGSTVVH G AA+ LL PRLGKF Sbjct: 215 SVLLVGIAYPITGHWVWDAGGWLYTMGFMDFAGSTVVHSVGGWAALAGAFLLGPRLGKF- 273 Query: 223 KEGKPVIIPGHNQVFTVLGVIILWFGWFGFNPGSALSPMGGFFGHVALTTNXXXXXXXXX 282 +G+P IPGHN F +LG +ILW GWFGFNPGS L+ ++A+TTN Sbjct: 274 VDGRPGAIPGHNMGFAMLGCLILWIGWFGFNPGSQLAADQAC-AYIAVTTNLAASAGGLT 332 Query: 283 XXXXSWLYFGKSDIPAMLNGVLAALVAITGACAFVEPWAAILIGFVAGAFTFMTSQWLER 342 SWL GK D+ ++NGVLA LV IT CA V W +++IG +AG + + ++ Sbjct: 333 ATFTSWLKDGKPDLTMVINGVLAGLVGITAGCAGVSYWGSVIIGGIAGILVVYSVAFFDK 392 Query: 343 AGLDDPIYAFSVHGIAGMWGAVSTGLFATPDLITKGALVGKAGLFYGGGFHQLGVQILGV 402 +DDP+ A SVH + G+WG ++ G F + GLFYGGG +QL +QI+G+ Sbjct: 393 IKIDDPVGAISVHLVNGVWGTLAVGFFNM-----------EKGLFYGGGINQLIIQIVGI 441 Query: 403 AGTFVFVAVMSFIILYVMKLVIGLRVTEEEELMGLDISEHGTYGYPEQMKLIAESES 459 F A+ SF++ ++K +G+RV+ EEE++GLDI EHG Y +K E++S Sbjct: 442 LAIGAFTAIFSFVVWAILKQTMGIRVSGEEEMIGLDIGEHGMEAYTGFVK---ETDS 495 >AF1746 [P] COG0004 Ammonia permease Length = 468 Score = 288 bits (736), Expect = 2e-77, Method: Compositional matrix adjust. Identities = 174/442 (39%), Positives = 234/442 (52%), Gaps = 47/442 (10%) Query: 31 PDLQIGLDTAFTFLAFILVFFMQAGFAMLEAGSVRMKNAGHVAGKTVLTLAIASLCFWAI 90 P+L + D + + LV FMQAGFAMLEAG R KN +V K ++ A+ SL F+A+ Sbjct: 33 PELPV--DFVWALICGFLVMFMQAGFAMLEAGFSRAKNVANVMMKNLMDFAVGSLAFFAV 90 Query: 91 XXXXXXXXXXXXXXXXXXLYGGDTQAASFDSLAF-----SDVTLNVKFLFQMAFAAVSLA 145 + G D Q + + F DV+ + F + FAA + Sbjct: 91 GFAL--------------MMGADWQGIAGTTGWFLAGESYDVSTIELWFFMLVFAATAAT 136 Query: 146 IVSGGMAERAKLSVYIVFGILFSVVIYPVVAHWVWGGGWLAE----------LGMQDYAG 195 IVSG +AER K SVY+V+ + S VIYP+ HW+WGGGWL+ G D+AG Sbjct: 137 IVSGSIAERPKFSVYLVYSAVVSAVIYPIYGHWLWGGGWLSSSEFMVKLGGGYGALDFAG 196 Query: 196 STVVHLTGATAAVVATILLKPRLGKFNKEGKPVIIPGHNQVFTVLGVIILWFGWFGFNPG 255 S VVH G A+ A +LL PRLGK++ +G P IPGHN F V+G ILWFGWFGFN G Sbjct: 197 SGVVHALGGYIALAAVMLLGPRLGKYDSDGNPRAIPGHNLAFAVIGTFILWFGWFGFNAG 256 Query: 256 SALSPMGGFFGHVALTTNXXXXXXXXXXXXXSWLYFGKSDIPAMLNGVLAALVAITGACA 315 S LS +A TN +WL GK D+ NG +A LVAIT CA Sbjct: 257 STLSAHELRVSIIASNTNLAAAAGAVTAMAITWLRNGKPDVGMTCNGAVAGLVAITAPCA 316 Query: 316 FVEPWAAILIGFVAGAFTFMTSQWLERAGLDDPIYAFSVHGIAGMWGAV--------STG 367 +V+PW++++IG +AG WLE+ GLDD + A VHG +G WG + S G Sbjct: 317 WVQPWSSVVIGTIAGFIATYGYWWLEKRGLDDVVGAIPVHGFSGTWGLIALGIFADGSYG 376 Query: 368 LFATPDLITKGALVGKAGLFYGGGFHQLGVQILGVAGTFVFVAVMSFIILYVMKLVIGLR 427 L+AT + G L G G F VQ++ F + F + +++K VIG+R Sbjct: 377 LYATESPLVTGLLYGNWGFFI--------VQLISAIVNFAWAFGTGFALFWILKKVIGIR 428 Query: 428 VTEEEELMGLDISEHGTYGYPE 449 V+ EEE++GLDI+EH YP Sbjct: 429 VSPEEEMLGLDIAEHAAVAYPN 450 >MA4207 [P] COG0004 Ammonia permease Length = 469 Score = 249 bits (637), Expect = 6e-66, Method: Compositional matrix adjust. Identities = 182/472 (38%), Positives = 239/472 (50%), Gaps = 46/472 (9%) Query: 9 FLAMITLMVYPVS--AFAADGPTAPDLQIGLDTAFTF----LAFILVFFMQAGFAMLEAG 62 FL +I ++ +S AFAA G+ TA TF LA LVFFM AGF+++E G Sbjct: 11 FLIIICMIFIALSSPAFAATAEENAVAIEGVQTALTFVWLLLASGLVFFMHAGFSLVETG 70 Query: 63 SVRMKNAGHVAGKTVLTLAIASLCFWAIXXXXXXXXXXXXXXXXXXLYGGDTQA-ASFDS 121 R KN ++ K +T+ + L +WA+ +YG D D Sbjct: 71 LTRSKNTANILMKNFMTIVLGILIYWAVGWGV--------------MYGADAAGLIGTDQ 116 Query: 122 --LAFSDVTLNVKFLFQMAFAAVSLAIVSGGMAERAKLSVYIVFGILFSVVIYPVVAHWV 179 L+ +D L + FQM FAA IVSG MAER Y+++ I+ VIYPV HWV Sbjct: 117 FFLSGADNALWNGWFFQMVFAATGATIVSGAMAERTNFKAYLIYCIMMVAVIYPVYGHWV 176 Query: 180 WGGGWLAELG-------------MQDYAGSTVVHLTGATAAVVATILLKPRLGKFNKEGK 226 W G LA L D+AGS VVH G +A+ +L+ R+GKF K+GK Sbjct: 177 WSGADLALLTGADSPIVQAIGVPSHDFAGSGVVHSIGGYSALAGVLLVGARIGKF-KDGK 235 Query: 227 PVIIPGHNQVFTVLGVIILWFGWFGFNPGSALSPMGGFFGHVALTTNXXXXXXXXXXXXX 286 V IPGHN LG +IL GW GFN GS L + V + T Sbjct: 236 AVPIPGHNLTIAFLGTLILALGWIGFNGGSTLDGNDPYMNLVVVNTFLAAAAGAVVTMLI 295 Query: 287 SWLYFGKSDIPAMLNGVLAALVAITGACAFVEPWAAILIGFVAGAFTFMTSQWLERA-GL 345 +W+ GK D NG+L LVAIT C V WAAI+IG +AG + + E + Sbjct: 296 TWMKTGKPDPSLTANGLLGGLVAITAPCGSVNNWAAIIIGAIAGIIIYAGVMFNENTLKV 355 Query: 346 DDPIYAFSVHGIAGMWGAVSTGLFATPDLITKGALVGKA------GLFYGGGFHQLGVQI 399 DDP+ A +VHG G WG +S GLF+ I G L A GLFYGGG L +Q+ Sbjct: 356 DDPVGAIAVHGYCGSWGLISVGLFSIG--IGNGILADAAYAAEVPGLFYGGGISLLLIQL 413 Query: 400 LGVAGTFVFVAVMSFIILYVMKLVIGLRVTEEEELMGLDISEHGTYGYPEQM 451 + V + V+ +SFII ++ V+GLRV+EEEE+MGLDI EHG YPE + Sbjct: 414 ISVLCSIVWAFGISFIIFKILDAVVGLRVSEEEEIMGLDICEHGIRAYPEYL 465 Database: COG Posted date: Aug 3, 2010 9:58 AM Number of letters in database: 38,378,431 Number of sequences in database: 115,334 Lambda K H 0.327 0.141 0.435 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 115334 Number of Hits to DB: 32,281,428 Number of extensions: 1284295 Number of successful extensions: 4526 Number of sequences better than 1.0e-05: 33 Number of HSP's gapped: 4374 Number of HSP's successfully gapped: 34 Length of query: 464 Length of database: 38,378,431 Length adjustment: 110 Effective length of query: 354 Effective length of database: 25,691,691 Effective search space: 9094858614 Effective search space used: 9094858614 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 bits) S2: 118 (50.1 bits)