Align Arabinose import ATP-binding protein AraG; EC 7.5.2.12 (characterized, see rationale)
to candidate BPHYT_RS20740 BPHYT_RS20740 D-ribose transporter ATP binding protein
Query= uniprot:B2SYR5 (512 letters) >FitnessBrowser__BFirm:BPHYT_RS20740 Length = 503 Score = 404 bits (1038), Expect = e-117 Identities = 221/496 (44%), Positives = 320/496 (64%), Gaps = 5/496 (1%) Query: 1 MSATLRFDNIGKVFPGVRALDGVSFDVNVGQVHGLMGENGAGKSTLLKILGGEYQPDSGR 60 M+ + + K FPGVRAL V F++ G+VH LMGENGAGKSTL+KIL G Y D+G Sbjct: 1 MTPLISVKRLSKRFPGVRALHEVQFELVAGEVHALMGENGAGKSTLMKILAGVYTRDTGE 60 Query: 61 VMIDGNEVRFTSAASSIAAGIAVIHQELQYVPDLTVAENLLLGQLPNS-LG-WVNKREAK 118 ++ +G V F S + A G+ +IHQELQ + LT+A+N+ +G+ P LG ++++ + Sbjct: 61 ILYEGQPVDFQSPREAQAVGVGIIHQELQLMNHLTIAQNMFIGREPRGRLGLFLDEDKLN 120 Query: 119 RFVRERLEAMGVALDPNAKLRKLSIAQRQMVEICKALLRNARVIALDEPTSSLSHRETEV 178 + L M V LDP A + L++A++QMVEI KAL ++RV+ +DEPTS+L+ E Sbjct: 121 AQAHDILARMHVTLDPRALVSSLTVARQQMVEIAKALSFDSRVLIMDEPTSALNDAEIAE 180 Query: 179 LFKLVRDLRADNRAMIYISHRMDEIYELCDACTIFRDGRKIASHPTLEGVTRDTIVSEMV 238 LF+++RDL+ +IYISH+MDE+ ++ D T+ RDG +A+ ++ T I+ MV Sbjct: 181 LFRIIRDLKKRGVGIIYISHKMDELKQIADRVTVLRDGEYVAT-VAVKDTTVQAIIGMMV 239 Query: 239 GREISDIY-NYSARPLGEVRFAAKGIEGHALAQPASFEVRRGEIVGFFGLVGAGRSELMH 297 GR ++D + GEV + L + SF +R+GEI+GF GL+GAGR+E+ Sbjct: 240 GRTLTDAAPSQHIANQGEVALEVTRLNAGPLVRDVSFALRKGEILGFAGLMGAGRTEVAR 299 Query: 298 LVYGADHKKGGELLLDGKPIKVRSAGEAIRHGIVLCPEDRKEEGIVAMATVSENINISCR 357 V+GAD + GE+++ G +R+ +A+ GI EDRK G+ +V NI +S Sbjct: 300 AVFGADPIESGEIVVKGVKATIRNPSDAVARGIGYLSEDRKRFGLATGMSVESNIVMSNL 359 Query: 358 RHYLRVGMFLDRKKEAETADRFIKLLKIKTPSRRQKIRFLSGGNQQKAILSRWLAEPDLK 417 R +L + FL R + +TA FI LL I+TPS Q++R LSGGNQQK ++++WL E D Sbjct: 360 RKFLSLNFFLRRTQIRKTAAHFINLLAIRTPSATQEVRLLSGGNQQKIVIAKWL-ERDCD 418 Query: 418 VVILDEPTRGIDVGAKHEIYNVIYQLAERGCAIVMISSELPEVLGVSDRIVVMRQGRISG 477 V+ DEPTRGIDVGAK EIY ++ LA++G AIVMISSELPE+L +SDRIVVM +GRI+G Sbjct: 419 VLFFDEPTRGIDVGAKSEIYKLLRSLADQGKAIVMISSELPEILRMSDRIVVMCEGRITG 478 Query: 478 ELTRKDATEQSVLSLA 493 EL AT++ ++ LA Sbjct: 479 ELAAAGATQERIMQLA 494 Score = 103 bits (258), Expect = 1e-26 Identities = 72/259 (27%), Positives = 133/259 (51%), Gaps = 6/259 (2%) Query: 252 PLGEVRFAAKGIEGHALAQPASFEVRRGEIVGFFGLVGAGRSELMHLVYGADHKKGGELL 311 PL V+ +K G FE+ GE+ G GAG+S LM ++ G + GE+L Sbjct: 3 PLISVKRLSKRFPGVRALHEVQFELVAGEVHALMGENGAGKSTLMKILAGVYTRDTGEIL 62 Query: 312 LDGKPIKVRSAGEAIRHGIVLCPEDRKEEGIVAMATVSENINISCRRHYLRVGMFLDRKK 371 +G+P+ +S EA G+ + ++ + ++ T+++N+ I R R+G+FLD K Sbjct: 63 YEGQPVDFQSPREAQAVGVGIIHQELQ---LMNHLTIAQNMFIG-REPRGRLGLFLDEDK 118 Query: 372 EAETADRFIKLLKIKTPSRRQKIRFLSGGNQQKAILSRWLAEPDLKVVILDEPTRGIDVG 431 A + + + T R + L+ QQ +++ L+ D +V+I+DEPT ++ Sbjct: 119 LNAQAHDILARMHV-TLDPRALVSSLTVARQQMVEIAKALSF-DSRVLIMDEPTSALNDA 176 Query: 432 AKHEIYNVIYQLAERGCAIVMISSELPEVLGVSDRIVVMRQGRISGELTRKDATEQSVLS 491 E++ +I L +RG I+ IS ++ E+ ++DR+ V+R G + KD T Q+++ Sbjct: 177 EIAELFRIIRDLKKRGVGIIYISHKMDELKQIADRVTVLRDGEYVATVAVKDTTVQAIIG 236 Query: 492 LALPQSSTALPGTQAAAQQ 510 + + ++ T +Q A Q Sbjct: 237 MMVGRTLTDAAPSQHIANQ 255 Lambda K H 0.320 0.136 0.385 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: 613 Number of extensions: 34 Number of successful extensions: 8 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: 512 Length of database: 503 Length adjustment: 34 Effective length of query: 478 Effective length of database: 469 Effective search space: 224182 Effective search space used: 224182 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