Align Ribose import ATP-binding protein RbsA 2, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose (characterized)
to candidate BWI76_RS27035 BWI76_RS27035 xylose ABC transporter ATP-binding protein
Query= TCDB::Q9X051 (523 letters) >FitnessBrowser__Koxy:BWI76_RS27035 Length = 513 Score = 441 bits (1135), Expect = e-128 Identities = 229/509 (44%), Positives = 344/509 (67%), Gaps = 6/509 (1%) Query: 12 LLEARNITKTFPGVIAVNNVTLQIYKGEVCALVGENGAGKSTLMKILAGVYP--DYEGQI 69 LLE +NITKTF V A++NV+L++ GEV +L GENG+GKSTLMK+L G+YP YEG+I Sbjct: 4 LLEMKNITKTFGAVKAIDNVSLRLNAGEVVSLCGENGSGKSTLMKVLCGIYPHGSYEGEI 63 Query: 70 FLEGKEVRFRNPREAQENGIALIPQELDLVPNLSSAENIFLSREPVNEFGVIEYQKMFEQ 129 G+ ++ + R+ + GIA+I QEL LV +L+ ENIFL E ++ G+++Y+ M + Sbjct: 64 IFSGETLQPGHIRDTERKGIAIIHQELALVKHLTVLENIFLGAE-ISRHGLLDYETMTLR 122 Query: 130 ASKLFSKLGVNIDPKTKVEDLSTSQQQMVAIAKALSLDAKIIIMDEPTSAIGKRETEQLF 189 KL +++ + I P T+V DL QQQ+V IAKAL+ +++I+DEPT+++ ++ET L Sbjct: 123 CEKLLAQVNLAISPDTRVGDLGLGQQQLVEIAKALNKQVRLLILDEPTASLTEQETAILL 182 Query: 190 NIIRSLKNEGKSVIYISHRLEEIFEIADRVVVMRDGRKVGEGPIEEFDHDKLVRLMVGRS 249 NIIR L+N G + IYISH+L E+ I+D + V+RDG+ +G + D ++ +MVGR Sbjct: 183 NIIRDLQNHGIACIYISHKLNEVKAISDTICVIRDGQHIGTRNADGMSEDDIITMMVGRE 242 Query: 250 IDQFFIKERATITDEIFRVEGIKLWS-LDRKKLLVDDVSFYVRKGEVLGIYGLVGAGRTE 308 + + E + DEI RVE + W ++R V+DVSF +R+GE+LGI GLVGAGRTE Sbjct: 243 LTALYPSEAHSCGDEILRVENLTAWHPVNRHIKRVNDVSFSLRRGEILGIAGLVGAGRTE 302 Query: 309 LLEAIFGAHPGRTEGKVFIGGKEIKIHSPRDAVKNGIGLVPEDRKTAGLILQMSVLHNIT 368 ++ +FG PGR +GK+FI G+ + IH+ + A+ GI +VPEDRK G++ M+V NIT Sbjct: 303 AVQCLFGVWPGRWQGKIFIDGQPVTIHTCQQAIAQGIAMVPEDRKKDGIVPVMAVGKNIT 362 Query: 369 LPSVVMKLIVRKFGLIDSQLEKEIVRSFIEKLNIKTPSPYQIVENLSGGNQQKVVLAKWL 428 L + + +D E+ ++ I++L IKT SP + LSGGNQQK +LA+ L Sbjct: 363 LAA--LNQFTGPLSSLDDAGEQLCIQQSIQRLKIKTSSPELAIGRLSGGNQQKAILARCL 420 Query: 429 AIKPKVLLLDEPTRGIDVNAKSEIYKLISEMAVSGMGVVMVSSELPEILAMSDRILVMSE 488 + P++L+LDEPTRGID+ AK EIYKLI+++ G+ V+++SSELPE+L +SDR+LVM E Sbjct: 421 LLNPRILILDEPTRGIDIGAKYEIYKLINQLVQQGIAVIVISSELPEVLGLSDRVLVMHE 480 Query: 489 GRKTAEFLREEVTEEDLLKAAIPRSVKVE 517 G+ A + + +T+E +++AA+ VE Sbjct: 481 GKLKANLINQGLTQEQVMEAALRSERHVE 509 Lambda K H 0.317 0.137 0.372 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: 626 Number of extensions: 33 Number of successful extensions: 11 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 523 Length of database: 513 Length adjustment: 35 Effective length of query: 488 Effective length of database: 478 Effective search space: 233264 Effective search space used: 233264 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 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