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 16017 b1900 fused L-arabinose transporter subunits of ABC superfamily: ATP-binding components (NCBI)
Query= uniprot:A0A1N7TX47 (495 letters) >FitnessBrowser__Keio:16017 Length = 504 Score = 327 bits (838), Expect = 6e-94 Identities = 190/467 (40%), Positives = 277/467 (59%), Gaps = 4/467 (0%) Query: 12 VAKAYAGVPALRDGRLSLRAGSVHALCGGNGAGKSTFLSILMGITQRDAGSILLNGAPVQ 71 + K + GV AL D AG VHAL G NGAGKST L IL G GS+++NG + Sbjct: 13 IGKTFPGVKALTDISFDCYAGQVHALMGENGAGKSTLLKILSGNYAPTTGSVVINGQEMS 72 Query: 72 FNRPSEALAAGIAMITQELEPIPYMTVAENIWLGREPRRAGCIVDNKALNRRTRELLDSL 131 F+ + AL AG+A+I QEL +P MTVAENI+LG+ P + G IV+ LN L L Sbjct: 73 FSDTTAALNAGVAIIYQELHLVPEMTVAENIYLGQLPHKGG-IVNRSLLNYEAGLQLKHL 131 Query: 132 EFDVDATSPMHRLSVAQIQLVEIAKAFSHDCQVMIMDEPTSAIGEHEAQTLFKAIRRLTA 191 D+D +P+ LS+ Q Q+VEIAKA + + +++ DEPTS++ E LF+ IR L Sbjct: 132 GMDIDPDTPLKYLSIGQWQMVEIAKALARNAKIIAFDEPTSSLSAREIDNLFRVIRELRK 191 Query: 192 QGAGIVYVSHRLSELAQIADDYSIFRDGAFVES-GRMADIDRDHLVRGIVGQELTRIDHK 250 +G I+YVSHR+ E+ ++D ++F+DG +V++ M +D D LV+ +VG+++ I Sbjct: 192 EGRVILYVSHRMEEIFALSDAITVFKDGRYVKTFTDMQQVDHDALVQAMVGRDIGDIYGW 251 Query: 251 VGRECAANTCLQVDNLSRAGEFHDISLQLRQGEILGIYGLMGSGRSEFLNCIYGLTVADS 310 R L++D + G ISL +R GEI+G++GL+G+GRSE + ++G T + Sbjct: 252 QPRSYGEER-LRLDAVKAPGVRTPISLAVRSGEIVGLFGLVGAGRSELMKGMFGGTQITA 310 Query: 311 GSVTLQGKPMPIGLPKATINAGMSLVTEDRKDSGLVLTGSILSNIALSA-YKRLSSWSLI 369 G V + +P+ I P I AGM L EDRK G++ S+ NI +SA K + +I Sbjct: 311 GQVYIDQQPIDIRKPSHAIAAGMMLCPEDRKAEGIIPVHSVRDNINISARRKHVLGGCVI 370 Query: 370 NARKETQLAEDMVKRLQIKTTSLELPVASMSGGNQQKVVLAKCLSTEPVCLLCDEPTRGI 429 N E A+ ++ L IKT E + ++SGGNQQK +L + LS E +L DEPTRGI Sbjct: 371 NNGWEENNADHHIRSLNIKTPGAEQLIMNLSGGNQQKAILGRWLSEEMKVILLDEPTRGI 430 Query: 430 DEGAKQEIYHLLDQFVRGGGAAIVVSSEAPELLHLSDRIAVFKGGRL 476 D GAK EIY+++ G A + SS+ PE+L ++DRI V + G + Sbjct: 431 DVGAKHEIYNVIYALAAQGVAVLFASSDLPEVLGVADRIVVMREGEI 477 Score = 75.1 bits (183), Expect = 5e-18 Identities = 59/212 (27%), Positives = 96/212 (45%), Gaps = 12/212 (5%) Query: 274 DISLQLRQGEILGIYGLMGSGRSEFLNCIYGLTVADSGSVTLQGKPMPIGLPKATINAGM 333 DIS G++ + G G+G+S L + G +GSV + G+ M A +NAG+ Sbjct: 25 DISFDCYAGQVHALMGENGAGKSTLLKILSGNYAPTTGSVVINGQEMSFSDTTAALNAGV 84 Query: 334 SLVTEDRKDSGLVLTGSILSNIALSAYKR---LSSWSLINARKETQLAEDMVKRLQIKTT 390 +++ ++ LV ++ NI L + + SL+N QL K L + Sbjct: 85 AIIYQELH---LVPEMTVAENIYLGQLPHKGGIVNRSLLNYEAGLQL-----KHLGMDID 136 Query: 391 SLELPVASMSGGNQQKVVLAKCLSTEPVCLLCDEPTRGIDEGAKQEIYHLLDQFVRGGGA 450 + P+ +S G Q V +AK L+ + DEPT + ++ ++ + + G Sbjct: 137 P-DTPLKYLSIGQWQMVEIAKALARNAKIIAFDEPTSSLSAREIDNLFRVIRELRKEGRV 195 Query: 451 AIVVSSEAPELLHLSDRIAVFKGGRLVTISTD 482 + VS E+ LSD I VFK GR V TD Sbjct: 196 ILYVSHRMEEIFALSDAITVFKDGRYVKTFTD 227 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: 591 Number of extensions: 28 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: 495 Length of database: 504 Length adjustment: 34 Effective length of query: 461 Effective length of database: 470 Effective search space: 216670 Effective search space used: 216670 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