Align ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale)
to candidate 17628 b3567 fused D-xylose transporter subunits of ABC superfamily: ATP-binding components (NCBI)
Query= uniprot:A0A0C4Y5F6 (540 letters) >FitnessBrowser__Keio:17628 Length = 513 Score = 359 bits (921), Expect = e-103 Identities = 208/487 (42%), Positives = 299/487 (61%), Gaps = 14/487 (2%) Query: 13 LLALRNICKTFPGVRALRKVELTAYAGEVHALMGENGAGKSTLMKILSGAYT-ADPGGEC 71 LL ++NI KTF V+A+ V L AGE+ +L GENG+GKSTLMK+L G Y GE Sbjct: 4 LLEMKNITKTFGSVKAIDNVCLRLNAGEIVSLCGENGSGKSTLMKVLCGIYPHGSYEGEI 63 Query: 72 HIDGQRVQIDGPQSARDLGVAVIYQELSLAPNLSVAENIYLGRALQRRGLVARGDMVRAC 131 G+ +Q + G+A+I+QEL+L L+V ENI+LG + G++ M C Sbjct: 64 IFAGEEIQASHIRDTERKGIAIIHQELALVKELTVLENIFLGNEITHNGIMDYDLMTLRC 123 Query: 132 APTLARLGADFSPAANVASLSIAQRQLVEIARAVHFEARILVMDEPTTPLSTHETDRLFA 191 LA++ SP V L + Q+QLVEIA+A++ + R+L++DEPT L+ ET L Sbjct: 124 QKLLAQVSLSISPDTRVGDLGLGQQQLVEIAKALNKQVRLLILDEPTASLTEQETSILLD 183 Query: 192 LIRQLRGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHLSQAALVKMMVGRDL 251 +IR L+ G+A +YISH++ E+ ++D + V+RDG +GT D A +S+ ++ MMVGR+L Sbjct: 184 IIRDLQQHGIACIYISHKLNEVKAISDTICVIRDGQHIGTRDAAGMSEDDIITMMVGREL 243 Query: 252 SGFYTK---THGQAVEREVMLSVRDVADG--RRVKGCSFDLRAGEVLGLAGLVGAGRTEL 306 + Y T G + R L+ + +RV SF L+ GE+LG+AGLVGAGRTE Sbjct: 244 TALYPNEPHTTGDEILRIEHLTAWHPVNRHIKRVNDVSFSLKRGEILGIAGLVGAGRTET 303 Query: 307 ARLVFGA-DARTRGEVRIANPAGSGGLVTLPAGGPRQAIDAGIAYLTEDRKLQGLFLDQS 365 + +FG + G++ I G V + +QAI GIA + EDRK G+ + Sbjct: 304 IQCLFGVWPGQWEGKIYI-----DGKQVDIR--NCQQAIAQGIAMVPEDRKRDGIVPVMA 356 Query: 366 VHENINLIVAARDALGLGRLNRTAARRRTTEAIDTLGIRVAHAQVNVGALSGGNQQKVML 425 V +NI L + G+ +L+ A ++ E+I L ++ + + +G LSGGNQQK +L Sbjct: 357 VGKNITLAALNKFTGGISQLDDAAEQKCILESIQQLKVKTSSPDLAIGRLSGGNQQKAIL 416 Query: 426 SRLLEIQPRVLILDEPTRGVDIGAKSEIYRLINALAQSGVAILMISSELPEVVGLCDRVL 485 +R L + PR+LILDEPTRG+DIGAK EIY+LIN L Q G+A+++ISSELPEV+GL DRVL Sbjct: 417 ARCLLLNPRILILDEPTRGIDIGAKYEIYKLINQLVQQGIAVIVISSELPEVLGLSDRVL 476 Query: 486 VMREGTL 492 VM EG L Sbjct: 477 VMHEGKL 483 Score = 84.3 bits (207), Expect = 1e-20 Identities = 63/247 (25%), Positives = 125/247 (50%), Gaps = 10/247 (4%) Query: 8 STKAPLLALRNICKTFPGVRALRKVELTAYA---GEVHALMGENGAGKSTLMKILSGAYT 64 +T +L + ++ P R +++V +++ GE+ + G GAG++ ++ L G + Sbjct: 253 TTGDEILRIEHLTAWHPVNRHIKRVNDVSFSLKRGEILGIAGLVGAGRTETIQCLFGVWP 312 Query: 65 ADPGGECHIDGQRVQIDGPQSARDLGVAVIYQELS---LAPNLSVAENIYLGRALQRRGL 121 G+ +IDG++V I Q A G+A++ ++ + P ++V +NI L + G Sbjct: 313 GQWEGKIYIDGKQVDIRNCQQAIAQGIAMVPEDRKRDGIVPVMAVGKNITLAALNKFTGG 372 Query: 122 VARGDMV---RACAPTLARLGADFS-PAANVASLSIAQRQLVEIARAVHFEARILVMDEP 177 +++ D + ++ +L S P + LS +Q +AR + RIL++DEP Sbjct: 373 ISQLDDAAEQKCILESIQQLKVKTSSPDLAIGRLSGGNQQKAILARCLLLNPRILILDEP 432 Query: 178 TTPLSTHETDRLFALIRQLRGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHL 237 T + ++ LI QL +G+A++ IS + E+ L+DRV V+ +G L +L Sbjct: 433 TRGIDIGAKYEIYKLINQLVQQGIAVIVISSELPEVLGLSDRVLVMHEGKLKANLINHNL 492 Query: 238 SQAALVK 244 +Q +++ Sbjct: 493 TQEQVME 499 Score = 67.4 bits (163), Expect = 1e-15 Identities = 65/236 (27%), Positives = 107/236 (45%), Gaps = 19/236 (8%) Query: 287 LRAGEVLGLAGLVGAGRTELARLVFGA--DARTRGEVRIANPAGSGGLVTLPAGGPRQAI 344 L AGE++ L G G+G++ L +++ G GE+ A + A R Sbjct: 27 LNAGEIVSLCGENGSGKSTLMKVLCGIYPHGSYEGEIIFAGEE-------IQASHIRDTE 79 Query: 345 DAGIAYLTEDRKLQGLFLDQSVHENINLIVAARDALGLGRLNRTAARRRTTEAIDTLGIR 404 GIA + ++ L + +V ENI L + G ++ R + + + + Sbjct: 80 RKGIAIIHQEL---ALVKELTVLENIFL---GNEITHNGIMDYDLMTLRCQKLLAQVSLS 133 Query: 405 VAHAQVNVGALSGGNQQKVMLSRLLEIQPRVLILDEPTRGVDIGAKSEIYRLINALAQSG 464 ++ VG L G QQ V +++ L Q R+LILDEPT + S + +I L Q G Sbjct: 134 IS-PDTRVGDLGLGQQQLVEIAKALNKQVRLLILDEPTASLTEQETSILLDIIRDLQQHG 192 Query: 465 VAILMISSELPEVVGLCDRVLVMREGTLAGEVRPAGSAAETQERIIALATGAAAAA 520 +A + IS +L EV + D + V+R+G G AG +++ II + G A Sbjct: 193 IACIYISHKLNEVKAISDTICVIRDGQHIGTRDAAGM---SEDDIITMMVGRELTA 245 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: 553 Number of extensions: 24 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 3 Length of query: 540 Length of database: 513 Length adjustment: 35 Effective length of query: 505 Effective length of database: 478 Effective search space: 241390 Effective search space used: 241390 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