Align ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale)
to candidate BWI76_RS18245 BWI76_RS18245 L-arabinose transporter ATP-binding protein
Query= uniprot:A0A0C4Y5F6 (540 letters) >FitnessBrowser__Koxy:BWI76_RS18245 Length = 504 Score = 370 bits (949), Expect = e-107 Identities = 220/489 (44%), Positives = 301/489 (61%), Gaps = 17/489 (3%) Query: 12 PLLALRNICKTFPGVRALRKVELTAYAGEVHALMGENGAGKSTLMKILSGAYTADPGGEC 71 P L+ I TFPGV+AL + YAG+VHALMGENGAGKSTL+KILSG Y G Sbjct: 6 PYLSFHGITMTFPGVKALSDISFGCYAGQVHALMGENGAGKSTLLKILSGNYIPT-AGSL 64 Query: 72 HIDGQRVQIDGPQSARDLGVAVIYQELSLAPNLSVAENIYLGRALQRRGLVARGDMVRAC 131 I GQ++ + A + GVA+IYQEL L P ++VAENIYLG+ + G+V R + Sbjct: 65 QIRGQQMTFNHTTEALNAGVAIIYQELHLIPEMTVAENIYLGQLPHKGGIVNRSLLNYEA 124 Query: 132 APTLARLGADFSPAANVASLSIAQRQLVEIARAVHFEARILVMDEPTTPLSTHETDRLFA 191 L LG D P + LSI Q Q+VEIA+A+ A+I+ DEPT+ LS E + LF Sbjct: 125 GLQLKHLGLDIDPETPLKYLSIGQWQMVEIAKALARNAKIIAFDEPTSSLSAREIENLFR 184 Query: 192 LIRQLRGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAH-LSQAALVKMMVGRD 250 +IR+LR EG I+Y+SHRM EI L+D +TV +DG +V T D ++ ALV+ MVGR+ Sbjct: 185 VIRELRQEGRVIIYVSHRMEEIFALSDAITVFKDGRYVRTFDNMQEVNHDALVQAMVGRE 244 Query: 251 LSGFY---TKTHGQAVEREVMLSVRDVADGRRVKGCSFDLRAGEVLGLAGLVGAGRTELA 307 L Y + +G+ ER + V+ A G R + S +R+GE++GL GLVGAGR+EL Sbjct: 245 LGNIYGWQPREYGK--ERLRLEQVK--APGVR-QPVSLSVRSGEIVGLFGLVGAGRSELM 299 Query: 308 RLVFGADARTRGEVRIANPAGSGGLVTLPAGGPRQAIDAGIAYLTEDRKLQGLFLDQSVH 367 + +FG T G+V I A + P QAI AG+ EDRK +G+ SV Sbjct: 300 KGLFGGSRITGGQVYIDGEA-------IDIRKPAQAIQAGMMLCPEDRKAEGIIPVHSVR 352 Query: 368 ENINLIVAARDALGLGRLNRTAARRRTTEAIDTLGIRVAHAQVNVGALSGGNQQKVMLSR 427 +NIN+ + L +N + + I +L I+ A+ + LSGGNQQK +L R Sbjct: 353 DNINISARRKHILAGCVINNAWEAQNADQHIKSLNIKTPGAEQLIMNLSGGNQQKAILGR 412 Query: 428 LLEIQPRVLILDEPTRGVDIGAKSEIYRLINALAQSGVAILMISSELPEVVGLCDRVLVM 487 L + +V++LDEPTRG+D+GAK EIY +I ALA SGVA++ SS+LPEV+G+ DR++VM Sbjct: 413 WLSEEMKVILLDEPTRGIDVGAKHEIYNVIYALAASGVAVVFASSDLPEVLGVADRIVVM 472 Query: 488 REGTLAGEV 496 REG +AGE+ Sbjct: 473 REGEIAGEL 481 Score = 78.2 bits (191), Expect = 7e-19 Identities = 62/223 (27%), Positives = 108/223 (48%), Gaps = 10/223 (4%) Query: 24 PGVRALRKVELTAYAGEVHALMGENGAGKSTLMKILSGAYTADPGGECHIDGQRVQIDGP 83 PGVR + V L+ +GE+ L G GAG+S LMK L G + GG+ +IDG+ + I P Sbjct: 269 PGVR--QPVSLSVRSGEIVGLFGLVGAGRSELMKGLFGG-SRITGGQVYIDGEAIDIRKP 325 Query: 84 QSARDLGVAVIYQELS---LAPNLSVAENIYLGRALQR--RGLVARGDMVRACAPTLARL 138 A G+ + ++ + P SV +NI + + G V A + Sbjct: 326 AQAIQAGMMLCPEDRKAEGIIPVHSVRDNINISARRKHILAGCVINNAWEAQNADQHIKS 385 Query: 139 GADFSPAAN--VASLSIAQRQLVEIARAVHFEARILVMDEPTTPLSTHETDRLFALIRQL 196 +P A + +LS +Q + R + E +++++DEPT + ++ +I L Sbjct: 386 LNIKTPGAEQLIMNLSGGNQQKAILGRWLSEEMKVILLDEPTRGIDVGAKHEIYNVIYAL 445 Query: 197 RGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHLSQ 239 G+A+++ S + E+ +ADR+ V+R+G G L H ++ Sbjct: 446 AASGVAVVFASSDLPEVLGVADRIVVMREGEIAGELLHEHANE 488 Lambda K H 0.320 0.136 0.382 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: 625 Number of extensions: 29 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: 540 Length of database: 504 Length adjustment: 35 Effective length of query: 505 Effective length of database: 469 Effective search space: 236845 Effective search space used: 236845 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 Sep 17 2021. 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