Align ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale)
to candidate 1937256 b4485 predicted sugar transporter subunit: ATP-binding component of ABC superfamily (NCBI)
Query= uniprot:A0A0C4Y5F6 (540 letters) >FitnessBrowser__Keio:1937256 Length = 500 Score = 345 bits (884), Expect = 3e-99 Identities = 201/496 (40%), Positives = 291/496 (58%), Gaps = 20/496 (4%) Query: 7 TSTKAPLLALRNICKTFPGVRALRKVELTAYAGEVHALMGENGAGKSTLMKILSGAYTAD 66 T +L + K FPGV+AL V+ + GE+ AL+GENGAGKSTL+K L+G Y AD Sbjct: 3 TDQHQEILRTEGLSKFFPGVKALDNVDFSLRRGEIMALLGENGAGKSTLIKALTGVYHAD 62 Query: 67 PGGECHIDGQRVQIDGPQSARDLGVAVIYQELSLAPNLSVAENIYLGRALQRRGLVARGD 126 G ++GQ + A+ LG+ +YQE++L PN+SVA+N+++GR +R GL+ R + Sbjct: 63 RG-TIWLEGQAISPKNTAHAQQLGIGTVYQEVNLLPNMSVADNLFIGREPKRFGLLRRKE 121 Query: 127 MVRACAPTLARLGADFSPAANVASLSIAQRQLVEIARAVHFEARILVMDEPTTPLSTHET 186 M + +A G + S+A +Q+V I RA+ A++L++DEPT L T E Sbjct: 122 MEKRATELMASYGFSLDVREPLNRFSVAMQQIVAICRAIDLSAKVLILDEPTASLDTQEV 181 Query: 187 DRLFALIRQLRGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHLSQAALVKMM 246 + LF L+RQLR G+++++++H + ++ +++DR+TVLR+G FVG + L Q LVKMM Sbjct: 182 ELLFDLMRQLRDRGVSLIFVTHFLDQVYQVSDRITVLRNGSFVGCRETCELPQIELVKMM 241 Query: 247 VGRDLSGFYTKTHGQAVEREVMLSVRDVAD----GRRVKGCSFDL--RAGEVLGLAGLVG 300 +GR+L TH +LS + VA G++ FDL R GE++GLAGL+G Sbjct: 242 LGRELD-----THALQRAGRTLLSDKPVAAFKNYGKKGTIAPFDLEVRPGEIVGLAGLLG 296 Query: 301 AGRTELARLVFGADARTRGEVRIANPAGSGGLVTLPAGGPRQAIDAGIAYLTEDRKLQGL 360 +GRTE A ++FG G I + P QA GI + EDRK G+ Sbjct: 297 SGRTETAEVIFGIKPADSGTALIKGKPQN-------LRSPHQASVLGIGFCPEDRKTDGI 349 Query: 361 FLDQSVHENINLIVAARDALGLGRLNRTAARRRTTEAIDTLGIRVAHAQVNVGALSGGNQ 420 SV ENI L + A+ L ++R + I LGIR + + LSGGNQ Sbjct: 350 IAAASVRENIILALQAQRG-WLRPISRKEQQEIAERFIRQLGIRTPSTEQPIEFLSGGNQ 408 Query: 421 QKVMLSRLLEIQPRVLILDEPTRGVDIGAKSEIYRLINALAQSGVAILMISSELPEVVGL 480 QKV+LSR L +P+ LILDEPTRG+D+GA +EI RLI L G+A+L+ISSEL E+VG Sbjct: 409 QKVLLSRWLLTRPQFLILDEPTRGIDVGAHAEIIRLIETLCADGLALLVISSELEELVGY 468 Query: 481 CDRVLVMREGTLAGEV 496 DRV++MR+ E+ Sbjct: 469 ADRVIIMRDRKQVAEI 484 Score = 70.1 bits (170), Expect = 2e-16 Identities = 64/238 (26%), Positives = 106/238 (44%), Gaps = 11/238 (4%) Query: 12 PLLALRNICKTFPGVRALRKVELTAYAGEVHALMGENGAGKSTLMKILSGAYTADPGGEC 71 P+ A +N K + +L GE+ L G G+G++ +++ G AD G Sbjct: 263 PVAAFKNYGKK----GTIAPFDLEVRPGEIVGLAGLLGSGRTETAEVIFGIKPAD-SGTA 317 Query: 72 HIDGQRVQIDGPQSARDLGVAVIYQELS---LAPNLSVAENIYLGRALQRRGL--VARGD 126 I G+ + P A LG+ ++ + SV ENI L QR L ++R + Sbjct: 318 LIKGKPQNLRSPHQASVLGIGFCPEDRKTDGIIAAASVRENIILALQAQRGWLRPISRKE 377 Query: 127 MVRACAPTLARLGADF-SPAANVASLSIAQRQLVEIARAVHFEARILVMDEPTTPLSTHE 185 + +LG S + LS +Q V ++R + + L++DEPT + Sbjct: 378 QQEIAERFIRQLGIRTPSTEQPIEFLSGGNQQKVLLSRWLLTRPQFLILDEPTRGIDVGA 437 Query: 186 TDRLFALIRQLRGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHLSQAALV 243 + LI L +G+A+L IS + E+ ADRV ++RD V + A LS A++ Sbjct: 438 HAEIIRLIETLCADGLALLVISSELEELVGYADRVIIMRDRKQVAEIPLAELSVPAIM 495 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: 577 Number of extensions: 24 Number of successful extensions: 7 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: 500 Length adjustment: 35 Effective length of query: 505 Effective length of database: 465 Effective search space: 234825 Effective search space used: 234825 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