Align Arabinose import ATP-binding protein AraG; EC 7.5.2.12 (characterized, see rationale)
to candidate Ac3H11_2881 Ribose ABC transport system, ATP-binding protein RbsA (TC 3.A.1.2.1)
Query= uniprot:B2SYR5 (512 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2881 Length = 496 Score = 353 bits (906), Expect = e-102 Identities = 203/497 (40%), Positives = 300/497 (60%), Gaps = 9/497 (1%) Query: 1 MSATLRFDNIGKVFPGVRALDGVSFDVNVGQVHGLMGENGAGKSTLLKILGGEYQPDSGR 60 MS + F N+ K F VR L GV F + G+V+GL+GENGAGKSTL+KIL G P +G Sbjct: 1 MSVAVEFRNVTKEFGPVRVLHGVGFALQPGRVYGLLGENGAGKSTLMKILAGYESPTTGE 60 Query: 61 VMIDGNEVRFTSAASSIAA--GIAVIHQELQYVPDLTVAENLLLGQLPNSLGWVNKREAK 118 V++DG VR S A GI +IHQE DLT+A+N+ LG +++ + + Sbjct: 61 VVVDG-AVRAPGGGSRAAEAQGIVLIHQEFNLADDLTIAQNIFLGHEIKRGLFLDDKAMR 119 Query: 119 RFVRERLEAMGVALDPNAKLRKLSIAQRQMVEICKALLRNARVIALDEPTSSLSHRETEV 178 RE L +G+ LDP+ ++RKL +A++Q+VEI +AL RNAR++ +DEPT++L+ ETE Sbjct: 120 EKTREALAKVGLPLDPDTRVRKLIVAEKQLVEIARALARNARLLIMDEPTATLTPGETER 179 Query: 179 LFKLVRDLRADNRAMIYISHRMDEIYELCDACTIFRDGRKIASHPTLEGVTRDTIVSEMV 238 LF L+ L+A +IYISH++DE+ D + RDG +A T VTR + + MV Sbjct: 180 LFALMAGLKAAGVTIIYISHKLDEVERTTDEVVVMRDGLLVAREAT-ASVTRRQMANLMV 238 Query: 239 GREISDIY--NYSARPLGEVRFAAKGIEGHALAQPASFEVRRGEIVGFFGLVGAGRSELM 296 GRE++D++ A G +G+ A+ FEVRRGEI+GF GLVGAGR+EL Sbjct: 239 GRELADLFPPKLPAPQDGAPAITVRGLTVPGWAEGVDFEVRRGEILGFAGLVGAGRTELF 298 Query: 297 HLVYGADHKKGGELLLDGKPIKVRSAGEAIRHGIVLCPEDRKEEGIVAMATVSENINISC 356 + G + G + + G+P++++S +A RHG+ EDRK +G+ + N+ + Sbjct: 299 EGLLGLRPRTAGTVEIAGQPVQLKSPRDAARHGLTYLSEDRKGKGLHVHFGLRPNLTLMA 358 Query: 357 RRHYLRVGMFLDRKKEAETADRFIKLLKIKTPSRRQKIRFLSGGNQQKAILSRWLAEPDL 416 Y + +LD E ++ I+T S + LSGGNQQK L++ L P Sbjct: 359 LERYAK--PWLDPAAEQAALREAVQEFGIRTGSLEVRASSLSGGNQQKLALAKVL-HPGP 415 Query: 417 KVVILDEPTRGIDVGAKHEIYNVIYQLAERGCAIVMISSELPEVLGVSDRIVVMRQGRIS 476 VV+LDEPTRG+DVGAK EIY+++ +LAE+G A+++ISSEL E++G+ R+ VMR GR+ Sbjct: 416 SVVVLDEPTRGVDVGAKREIYHLVQRLAEQGLAVIVISSELMELIGLCHRVAVMRAGRLQ 475 Query: 477 GELTRKDATEQSVLSLA 493 L TE+ +++ A Sbjct: 476 TTLQEPHLTEEELIAHA 492 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: 623 Number of extensions: 29 Number of successful extensions: 10 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: 512 Length of database: 496 Length adjustment: 34 Effective length of query: 478 Effective length of database: 462 Effective search space: 220836 Effective search space used: 220836 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