Align D-ribose transporter ATP-binding protein; SubName: Full=Putative xylitol transport system ATP-binding protein; SubName: Full=Sugar ABC transporter ATP-binding protein (characterized, see rationale)
to candidate 1937256 b4485 predicted sugar transporter subunit: ATP-binding component of ABC superfamily (NCBI)
Query= uniprot:A0A1N7TX47 (495 letters) >FitnessBrowser__Keio:1937256 Length = 500 Score = 313 bits (802), Expect = 9e-90 Identities = 173/488 (35%), Positives = 284/488 (58%), Gaps = 3/488 (0%) Query: 6 LLQAEHVAKAYAGVPALRDGRLSLRAGSVHALCGGNGAGKSTFLSILMGITQRDAGSILL 65 +L+ E ++K + GV AL + SLR G + AL G NGAGKST + L G+ D G+I L Sbjct: 9 ILRTEGLSKFFPGVKALDNVDFSLRRGEIMALLGENGAGKSTLIKALTGVYHADRGTIWL 68 Query: 66 NGAPVQFNRPSEALAAGIAMITQELEPIPYMTVAENIWLGREPRRAGCIVDNKALNRRTR 125 G + + A GI + QE+ +P M+VA+N+++GREP+R G ++ K + +R Sbjct: 69 EGQAISPKNTAHAQQLGIGTVYQEVNLLPNMSVADNLFIGREPKRFG-LLRRKEMEKRAT 127 Query: 126 ELLDSLEFDVDATSPMHRLSVAQIQLVEIAKAFSHDCQVMIMDEPTSAIGEHEAQTLFKA 185 EL+ S F +D P++R SVA Q+V I +A +V+I+DEPT+++ E + LF Sbjct: 128 ELMASYGFSLDVREPLNRFSVAMQQIVAICRAIDLSAKVLILDEPTASLDTQEVELLFDL 187 Query: 186 IRRLTAQGAGIVYVSHRLSELAQIADDYSIFRDGAFVESGRMADIDRDHLVRGIVGQEL- 244 +R+L +G +++V+H L ++ Q++D ++ R+G+FV ++ + LV+ ++G+EL Sbjct: 188 MRQLRDRGVSLIFVTHFLDQVYQVSDRITVLRNGSFVGCRETCELPQIELVKMMLGRELD 247 Query: 245 TRIDHKVGRECAANTCLQV-DNLSRAGEFHDISLQLRQGEILGIYGLMGSGRSEFLNCIY 303 T + GR ++ + N + G L++R GEI+G+ GL+GSGR+E I+ Sbjct: 248 THALQRAGRTLLSDKPVAAFKNYGKKGTIAPFDLEVRPGEIVGLAGLLGSGRTETAEVIF 307 Query: 304 GLTVADSGSVTLQGKPMPIGLPKATINAGMSLVTEDRKDSGLVLTGSILSNIALSAYKRL 363 G+ ADSG+ ++GKP + P G+ EDRK G++ S+ NI L+ + Sbjct: 308 GIKPADSGTALIKGKPQNLRSPHQASVLGIGFCPEDRKTDGIIAAASVRENIILALQAQR 367 Query: 364 SSWSLINARKETQLAEDMVKRLQIKTTSLELPVASMSGGNQQKVVLAKCLSTEPVCLLCD 423 I+ +++ ++AE +++L I+T S E P+ +SGGNQQKV+L++ L T P L+ D Sbjct: 368 GWLRPISRKEQQEIAERFIRQLGIRTPSTEQPIEFLSGGNQQKVLLSRWLLTRPQFLILD 427 Query: 424 EPTRGIDEGAKQEIYHLLDQFVRGGGAAIVVSSEAPELLHLSDRIAVFKGGRLVTISTDT 483 EPTRGID GA EI L++ G A +V+SSE EL+ +DR+ + + + V Sbjct: 428 EPTRGIDVGAHAEIIRLIETLCADGLALLVISSELEELVGYADRVIIMRDRKQVAEIPLA 487 Query: 484 ALSQEALL 491 LS A++ Sbjct: 488 ELSVPAIM 495 Score = 68.9 bits (167), Expect = 4e-16 Identities = 56/218 (25%), Positives = 92/218 (42%), Gaps = 5/218 (2%) Query: 27 LSLRAGSVHALCGGNGAGKSTFLSILMGITQRDAGSILLNGAPVQFNRPSEALAAGIAMI 86 L +R G + L G G+G++ ++ GI D+G+ L+ G P P +A GI Sbjct: 281 LEVRPGEIVGLAGLLGSGRTETAEVIFGIKPADSGTALIKGKPQNLRSPHQASVLGIGFC 340 Query: 87 TQELEP---IPYMTVAENIWLGREPRRAGCI-VDNKALNRRTRELLDSLEFDVDATS-PM 141 ++ + I +V ENI L + +R + K + L +T P+ Sbjct: 341 PEDRKTDGIIAAASVRENIILALQAQRGWLRPISRKEQQEIAERFIRQLGIRTPSTEQPI 400 Query: 142 HRLSVAQIQLVEIAKAFSHDCQVMIMDEPTSAIGEHEAQTLFKAIRRLTAQGAGIVYVSH 201 LS Q V +++ Q +I+DEPT I + + I L A G ++ +S Sbjct: 401 EFLSGGNQQKVLLSRWLLTRPQFLILDEPTRGIDVGAHAEIIRLIETLCADGLALLVISS 460 Query: 202 RLSELAQIADDYSIFRDGAFVESGRMADIDRDHLVRGI 239 L EL AD I RD V +A++ ++ I Sbjct: 461 ELEELVGYADRVIIMRDRKQVAEIPLAELSVPAIMNAI 498 Lambda K H 0.319 0.135 0.381 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: 525 Number of extensions: 27 Number of successful extensions: 6 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: 495 Length of database: 500 Length adjustment: 34 Effective length of query: 461 Effective length of database: 466 Effective search space: 214826 Effective search space used: 214826 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