Align ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale)
to candidate WP_083529580.1 AS188_RS10235 sugar ABC transporter ATP-binding protein
Query= uniprot:A0A0C4Y5F6 (540 letters) >NCBI__GCF_001482365.1:WP_083529580.1 Length = 492 Score = 346 bits (887), Expect = 1e-99 Identities = 208/479 (43%), Positives = 287/479 (59%), Gaps = 11/479 (2%) Query: 16 LRNICKTFPGVRALRKVELTAYAGEVHALMGENGAGKSTLMKILSGAYTADPGGECHIDG 75 +R I K F R L+ V+ AGEVH L GENGAGKSTLMKIL G Y+AD GE + G Sbjct: 1 MRGIEKAFGVNRVLKGVDFEVLAGEVHTLAGENGAGKSTLMKILQGVYSAD-AGEIFVGG 59 Query: 76 QRVQIDGPQSARDLGVAVIYQELSLAPNLSVAENIYLGRALQRR-GLVARGDMVRACAPT 134 V ID P +AR+ GV +++QE SL P LSVA+N++L R + GL+ MV Sbjct: 60 NPVTIDSPITAREAGVGMVFQEFSLVPTLSVAQNVFLNREPRNAMGLIDEDTMVEQTRAI 119 Query: 135 LARLGADFSPAANVASLSIAQRQLVEIARAVHFEARILVMDEPTTPLSTHETDRLFALIR 194 P V LS A QL EIA+AV AR+L++DEPT LS E++ LF LI+ Sbjct: 120 FETFEVPVDPRTPVERLSTAYWQLTEIAKAVSQNARVLILDEPTASLSKKESEILFDLIK 179 Query: 195 QLRGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHLSQAALVKMMVGRDLSGF 254 +L +G+ I+YISHRM EI ++ DR+TV+RDG V T ++ LV+ ++GR L Sbjct: 180 RLTSQGIGIVYISHRMEEIYQVTDRITVMRDGAVVLTDHATSITPEDLVEAIIGRRLENA 239 Query: 255 YT-KTHGQAVEREVMLSVRDVADGRRVKGCSFDLRAGEVLGLAGLVGAGRTELARLVFGA 313 +TH L V+ ++ ++ SF + GEVLGLAGL+G+GRTELAR +FG Sbjct: 240 LAYETHVVDRSGTPRLEVKRLSTDHGLEDVSFTVHPGEVLGLAGLMGSGRTELARALFGI 299 Query: 314 DARTRGEVRIANPAGSGGLVTLPAGGPRQAIDAGIAYLTEDRKLQGLFLDQSVHENINLI 373 D GE+ I G VT+ P A++AG + EDR+ QGL L SV +N+ L Sbjct: 300 DKHRDGEILI-----DGRPVTVT--DPVSAMEAGFGLVPEDRREQGLVLSHSVRDNLLLP 352 Query: 374 VAARDALGLGRLNRTAARRRTTEAIDTLGIRVAHAQVNVGALSGGNQQKVMLSRLLEIQP 433 + +R G ++ +RR + + ++ A + + LSGGNQQKV+L R + +P Sbjct: 353 LLSRFRKG-PLMDEGRSRRFVQDVLTKFEVKGASPGLEIRLLSGGNQQKVVLGRWVSTEP 411 Query: 434 RVLILDEPTRGVDIGAKSEIYRLINALAQSGVAILMISSELPEVVGLCDRVLVMREGTL 492 +VLILDEPT G+DIG K E+ LI LA+SG A+++ISSEL E++ + DRVLV+R+G L Sbjct: 412 KVLILDEPTAGIDIGTKGEVIELIRDLARSGTAVILISSELAELLAVSDRVLVLRKGRL 470 Score = 89.0 bits (219), Expect = 4e-22 Identities = 70/225 (31%), Positives = 109/225 (48%), Gaps = 7/225 (3%) Query: 29 LRKVELTAYAGEVHALMGENGAGKSTLMKILSGAYTADPGGECHIDGQRVQIDGPQSARD 88 L V T + GEV L G G+G++ L + L G GE IDG+ V + P SA + Sbjct: 266 LEDVSFTVHPGEVLGLAGLMGSGRTELARALFGI-DKHRDGEILIDGRPVTVTDPVSAME 324 Query: 89 LGVAVIYQ---ELSLAPNLSVAENIYLGRALQ-RRG-LVARGDMVRACAPTLARLGAD-F 142 G ++ + E L + SV +N+ L + R+G L+ G R L + Sbjct: 325 AGFGLVPEDRREQGLVLSHSVRDNLLLPLLSRFRKGPLMDEGRSRRFVQDVLTKFEVKGA 384 Query: 143 SPAANVASLSIAQRQLVEIARAVHFEARILVMDEPTTPLSTHETDRLFALIRQLRGEGMA 202 SP + LS +Q V + R V E ++L++DEPT + + LIR L G A Sbjct: 385 SPGLEIRLLSGGNQQKVVLGRWVSTEPKVLILDEPTAGIDIGTKGEVIELIRDLARSGTA 444 Query: 203 ILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHLSQAALVKMMV 247 ++ IS +AE+ ++DRV VLR G TLDR+ + +++ + Sbjct: 445 VILISSELAELLAVSDRVLVLRKGRLHKTLDRSEIHDEESLQLTI 489 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: 623 Number of extensions: 42 Number of successful extensions: 10 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: 492 Length adjustment: 35 Effective length of query: 505 Effective length of database: 457 Effective search space: 230785 Effective search space used: 230785 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 24 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