Align ABC transporter related (characterized, see rationale)
to candidate 206505 DVU1070 branched chain amino acid ABC transporter, ATP-binding protein (TIGR)
Query= uniprot:A0KWY5 (499 letters) >FitnessBrowser__DvH:206505 Length = 524 Score = 233 bits (595), Expect = 9e-66 Identities = 149/473 (31%), Positives = 251/473 (53%), Gaps = 16/473 (3%) Query: 4 ILELKQISKHYPGVKALEDVSLRLFAGEVHALLGENGAGKSTLVKVMTGAQSKDMGDILF 63 ++ L+ I K + V+A D++L + G + ALLGENGAGKSTL+ +++G ++D G I Sbjct: 34 VVRLEGIGKSFGPVRANHDITLDIVPGRIKALLGENGAGKSTLMSILSGRLAQDTGIIHV 93 Query: 64 LGEPQHFNTPMDAQKAGISTVYQEVNLVPNLTVAQNLFLGYEPRRLGLIHFKKMYADARA 123 GE F +P DA KAGI VYQ LV ++TVA+N+ LG L +H ++ A+ A Sbjct: 94 DGEAVRFRSPKDALKAGIGMVYQHFMLVDSMTVAENVLLGQSGAWLSPVHMSRVVAELAA 153 Query: 124 VLTQFKLDIDVSAPLSDYSIAVQQLIAIARGVAMSAKVLVLDEPTASLDAKEVQVLFGIL 183 ++ LDID +A + D S+ +Q + I + + ++VL+LDEPTA L E + LF L Sbjct: 154 ---RYGLDIDPAARVCDLSMGERQRVEILKLLYRDSRVLILDEPTAVLTPGETEQLFEAL 210 Query: 184 NQLKAKGVAIVFITHFLDQVYQISDRITVLRNGQFIGEYLTAELP-QPKLIEAMLGRS-L 241 +++ G AIVFI+H + +V ++D I +LR G+ + E+ +E+P + +L M+GR + Sbjct: 211 HRMAENGKAIVFISHKMQEVLALADEIAILRRGEVVDEFHESEVPGEAELANRMVGREVI 270 Query: 242 QEQLVDKQEKERTVTRAEAVLLSLEDVSVKGSIQSMNLTVPKGQAVGLAGLLGSGRSEVC 301 E + E V + + ++ ++ V KG+ +AG+ G+G+ E+ Sbjct: 271 LEVAAEPLEPGDRVLHVDGL--------AGDGLKGLSFEVRKGEVFAIAGVAGNGQRELV 322 Query: 302 NAVFGLDLVDSGSIHLAGQKLNLSQPVDAISAGIALCPEDRKIDGIIGPLSIRENIILAL 361 V GL G + L G G+A PEDR+ L + +N +L Sbjct: 323 ECVTGLRRPAEGEVELLGIPWRQFFTKAPRQGGLAYIPEDRQGLATCLSLDLVDNFLLTA 382 Query: 362 QARIGWWRYLSNTRQQEIAQFFIDKLQIATPDADKPIEQLSGGNQQKVILARWLAIEPIL 421 + +L A+ + + + A+ P LSGGN QK+++ R +P L Sbjct: 383 RGCFTRGPFLDRKSADAAARDILAEYNVQPGRAEAPARSLSGGNLQKLVVGREFYRKPSL 442 Query: 422 LVLDEPTRGIDIGAHAEI-VKLIRTLCDEGMSLLVASSELDELVAFSNKVVVL 473 +V + PT+G+DI A E+ +L+ G +L+ S +L+E++A +++V V+ Sbjct: 443 IVAENPTQGLDIAATEEVWARLLEVRSHAG--VLLVSGDLNEVLALADRVAVM 493 Score = 72.8 bits (177), Expect = 3e-17 Identities = 56/239 (23%), Positives = 115/239 (48%), Gaps = 18/239 (7%) Query: 255 VTRAEAVLLSLEDVSVKGSIQSMNLTVPKGQAVGLAGLLGSGRSEVCNAVFGLDLVDSGS 314 V R E + S V I L + G+ L G G+G+S + + + G D+G Sbjct: 34 VVRLEGIGKSFGPVRANHDI---TLDIVPGRIKALLGENGAGKSTLMSILSGRLAQDTGI 90 Query: 315 IHLAGQKLNLSQPVDAISAGIALCPEDRKIDGIIGPLSIRENIILALQARIGWWR---YL 371 IH+ G+ + P DA+ AGI + + + + +++ EN++L + G W ++ Sbjct: 91 IHVDGEAVRFRSPKDALKAGIGMVYQHFML---VDSMTVAENVLLG---QSGAWLSPVHM 144 Query: 372 SNTRQQEIAQFFIDKLQIATPDADKPIEQLSGGNQQKVILARWLAIEPILLVLDEPTRGI 431 S + A++ +D D + LS G +Q+V + + L + +L+LDEPT + Sbjct: 145 SRVVAELAARYGLDI------DPAARVCDLSMGERQRVEILKLLYRDSRVLILDEPTAVL 198 Query: 432 DIGAHAEIVKLIRTLCDEGMSLLVASSELDELVAFSNKVVVLRDRYAVRELSGAELTSQ 490 G ++ + + + + G +++ S ++ E++A ++++ +LR V E +E+ + Sbjct: 199 TPGETEQLFEALHRMAENGKAIVFISHKMQEVLALADEIAILRRGEVVDEFHESEVPGE 257 Score = 56.2 bits (134), Expect = 3e-12 Identities = 54/213 (25%), Positives = 98/213 (46%), Gaps = 19/213 (8%) Query: 20 LEDVSLRLFAGEVHALLGENGAGKSTLVKVMTGAQSKDMGDILFLGEP-QHFNTPMDAQ- 77 L+ +S + GEV A+ G G G+ LV+ +TG + G++ LG P + F T Q Sbjct: 295 LKGLSFEVRKGEVFAIAGVAGNGQRELVECVTGLRRPAEGEVELLGIPWRQFFTKAPRQG 354 Query: 78 --------KAGISTVYQEVNLVPN-LTVAQNLFLGYEPRRLGLIHFKKMYADARAVLTQF 128 + G++T ++LV N L A+ F R + K A AR +L ++ Sbjct: 355 GLAYIPEDRQGLATCLS-LDLVDNFLLTARGCFT-----RGPFLDRKSADAAARDILAEY 408 Query: 129 KLDID-VSAPLSDYSIAVQQLIAIARGVAMSAKVLVLDEPTASLDAKEVQVLFGILNQLK 187 + AP S Q + + R ++V + PT LD + ++ L +++ Sbjct: 409 NVQPGRAEAPARSLSGGNLQKLVVGREFYRKPSLIVAENPTQGLDIAATEEVWARLLEVR 468 Query: 188 AKGVAIVFITHFLDQVYQISDRITVLRNGQFIG 220 + ++ ++ L++V ++DR+ V+ G FIG Sbjct: 469 SHA-GVLLVSGDLNEVLALADRVAVMYRGCFIG 500 Lambda K H 0.319 0.136 0.377 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 590 Number of extensions: 30 Number of successful extensions: 9 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 4 Number of HSP's successfully gapped: 3 Length of query: 499 Length of database: 524 Length adjustment: 35 Effective length of query: 464 Effective length of database: 489 Effective search space: 226896 Effective search space used: 226896 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory