Align ABC transporter related; Flags: Precursor (characterized, see rationale)
to candidate WP_078427103.1 BK574_RS00955 ABC transporter ATP-binding protein
Query= uniprot:B2T9V9 (510 letters) >NCBI__GCF_002019605.1:WP_078427103.1 Length = 509 Score = 248 bits (633), Expect = 4e-70 Identities = 155/484 (32%), Positives = 256/484 (52%), Gaps = 16/484 (3%) Query: 14 VVEALEVTKRFGSTAALNDVSIRVMPGESHALVGRNGAGKSTLVSILTGLRKPDTGEVRF 73 V+E ++ K F A ++V+++V GE HAL+G NGAGKSTL+++L GL +P+ GE+ Sbjct: 4 VIEMKDIRKEFPGIVANDNVTLQVKQGEIHALLGENGAGKSTLMNVLFGLYQPEKGEILV 63 Query: 74 SGAAAPSIADRDAWRERVACVYQHSTIIRDLSVAENLFINRQPLRGGVIDWQAMRRDARA 133 G A R + V+QH ++ +V EN+ + ++P GG I+ + + Sbjct: 64 KGKPVKITDPNVANRLGIGMVHQHFMLVEKFTVTENIILGKEPTAGGKINIKKAAKAVET 123 Query: 134 LLDHWKIDVREDARAGDLSVEARQLVEIARALSYGARFIILDEPTAQLDGDEIKRLFRRI 193 + + + V A+ D+SV +Q VEI + L GA +I DEPTA L EI L + + Sbjct: 124 ISKQYGLAVDPYAKIQDISVGMQQRVEILKTLYRGAEILIFDEPTAALTPQEITELIQIM 183 Query: 194 SELQREGVTFLFISHHLQEVYEICQAVTVLRDARHIVSAPVSALPREQLIEAMTGERGGL 253 +L EG + + I+H L+E+ E+C TV+R R I + +S + L M G Sbjct: 184 KKLVSEGKSIILITHKLKEIMEVCDRCTVIRRGRGIGTVDISESTPDSLAAMMVGREVNF 243 Query: 254 AVADAAARGALPADTAVALELKELTGADYEGVS------FTVKRGEVVGLTGATSSGRTS 307 +V A+ P D L++K+L D ++ V GE++G+ G +G+T Sbjct: 244 SVEKDPAQ---PKD--AVLQIKDLVVKDSRDITAVNDLHLEVHAGEILGVAGVDGNGQTE 298 Query: 308 VAEAIAGLRAAKRGTISVDGAILPPGDVPASL-AHGIGCVPKDRHHEGLVLTQSVAENAS 366 + EAI GLR G I ++G + G P + G+G +P+DRH GLVL +V EN Sbjct: 299 LIEAITGLRKPTGGNIQLNGQDI-TGLTPRKITGAGVGHIPQDRHKHGLVLDFTVGENIV 357 Query: 367 MT--IARVLGKFGIAAPAKKNAFGQKMIDALGIVAQGPEHVVSGLSGGNQQKVVMARALA 424 + + G+ + ++I+ + + LSGGNQQK ++AR + Sbjct: 358 LQTYYQKPYSTSGVLNFNEIYKKANELIEDYDVRTPSEHTLARALSGGNQQKAIIAREVD 417 Query: 425 TNPNVLVLIDPTAGVDVKSKEALLSVVDRVREEGKAVLVVSGELDD-LRTCDRVLVMFRG 483 +P++L+ PT G+DV + E++ + + R++GKAVL++S ELD+ L DR+ V++ G Sbjct: 418 RSPDLLIAAQPTRGLDVGAIESIHHRLVKERDKGKAVLLISLELDEVLNVSDRIAVIYEG 477 Query: 484 RVAA 487 ++ A Sbjct: 478 KIVA 481 Score = 73.2 bits (178), Expect = 2e-17 Identities = 61/240 (25%), Positives = 109/240 (45%), Gaps = 14/240 (5%) Query: 20 VTKRFGSTAALNDVSIRVMPGESHALVGRNGAGKSTLVSILTGLRKPDTGEVRFSGAAAP 79 V K A+ND+ + V GE + G +G G++ L+ +TGLRKP G ++ +G Sbjct: 263 VVKDSRDITAVNDLHLEVHAGEILGVAGVDGNGQTELIEAITGLRKPTGGNIQLNGQDIT 322 Query: 80 SIADRDAWRERVACV----YQHSTIIRDLSVAENLFIN---RQPLR-GGVIDWQAMRRDA 131 + R V + ++H ++ D +V EN+ + ++P GV+++ + + A Sbjct: 323 GLTPRKITGAGVGHIPQDRHKHGLVL-DFTVGENIVLQTYYQKPYSTSGVLNFNEIYKKA 381 Query: 132 RALLDHWKIDVR---EDARAGDLSVEARQLVEIARALSYGARFIILDEPTAQLDGDEIKR 188 L++ + DVR E A LS +Q IAR + +I +PT LD I+ Sbjct: 382 NELIEDY--DVRTPSEHTLARALSGGNQQKAIIAREVDRSPDLLIAAQPTRGLDVGAIES 439 Query: 189 LFRRISELQREGVTFLFISHHLQEVYEICQAVTVLRDARHIVSAPVSALPREQLIEAMTG 248 + R+ + + +G L IS L EV + + V+ + + + +L M G Sbjct: 440 IHHRLVKERDKGKAVLLISLELDEVLNVSDRIAVIYEGKIVAIVDADKTNENELGLLMAG 499 Lambda K H 0.318 0.134 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: 567 Number of extensions: 40 Number of successful extensions: 9 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 510 Length of database: 509 Length adjustment: 34 Effective length of query: 476 Effective length of database: 475 Effective search space: 226100 Effective search space used: 226100 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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