Align Arabinose import ATP-binding protein AraG; EC 7.5.2.12 (characterized, see rationale)
to candidate H281DRAFT_06298 H281DRAFT_06298 L-arabinose ABC transporter ATP-binding protein
Query= uniprot:B2SYR5 (512 letters) >FitnessBrowser__Burk376:H281DRAFT_06298 Length = 519 Score = 957 bits (2475), Expect = 0.0 Identities = 490/512 (95%), Positives = 502/512 (98%) Query: 1 MSATLRFDNIGKVFPGVRALDGVSFDVNVGQVHGLMGENGAGKSTLLKILGGEYQPDSGR 60 +SATLRFDNIGKVFPGVRALDGVSFDVNVGQVHGLMGENGAGKSTLLKILGGEYQPDSGR Sbjct: 8 VSATLRFDNIGKVFPGVRALDGVSFDVNVGQVHGLMGENGAGKSTLLKILGGEYQPDSGR 67 Query: 61 VMIDGNEVRFTSAASSIAAGIAVIHQELQYVPDLTVAENLLLGQLPNSLGWVNKREAKRF 120 VMIDG EVRFTSAASSIAAGIAVIHQELQYVPDLTVAENLLLGQLPNS GWVNKR+AKRF Sbjct: 68 VMIDGKEVRFTSAASSIAAGIAVIHQELQYVPDLTVAENLLLGQLPNSFGWVNKRDAKRF 127 Query: 121 VRERLEAMGVALDPNAKLRKLSIAQRQMVEICKALLRNARVIALDEPTSSLSHRETEVLF 180 VRERLEAMGVALDPNAKLRKLSIAQRQMVEICKALLRNARVIALDEPTSSLSHRETEVLF Sbjct: 128 VRERLEAMGVALDPNAKLRKLSIAQRQMVEICKALLRNARVIALDEPTSSLSHRETEVLF 187 Query: 181 KLVRDLRADNRAMIYISHRMDEIYELCDACTIFRDGRKIASHPTLEGVTRDTIVSEMVGR 240 KLVRDLRADNRAMIYISHRMDEIYELCDACTIFRDGRKIASHPTLEGV+RDTIVSEMVGR Sbjct: 188 KLVRDLRADNRAMIYISHRMDEIYELCDACTIFRDGRKIASHPTLEGVSRDTIVSEMVGR 247 Query: 241 EISDIYNYSARPLGEVRFAAKGIEGHALAQPASFEVRRGEIVGFFGLVGAGRSELMHLVY 300 EISDIYNYS RPLGEVRFAAK IEGHAL+QPASFEVRRGEIVGFFGLVGAGRSELMHLVY Sbjct: 248 EISDIYNYSERPLGEVRFAAKAIEGHALSQPASFEVRRGEIVGFFGLVGAGRSELMHLVY 307 Query: 301 GADHKKGGELLLDGKPIKVRSAGEAIRHGIVLCPEDRKEEGIVAMATVSENINISCRRHY 360 G +HKKGGEL+LDGK I+V+SAGEAIRHGIVLCPEDRKEEGIVAMATVSENINISCRRHY Sbjct: 308 GTEHKKGGELVLDGKTIRVKSAGEAIRHGIVLCPEDRKEEGIVAMATVSENINISCRRHY 367 Query: 361 LRVGMFLDRKKEAETADRFIKLLKIKTPSRRQKIRFLSGGNQQKAILSRWLAEPDLKVVI 420 LR G+FLDRKKEAETADRFIKLLKIKTPSRRQKIRFLSGGNQQKAILSRWLAEPDLKVVI Sbjct: 368 LRAGVFLDRKKEAETADRFIKLLKIKTPSRRQKIRFLSGGNQQKAILSRWLAEPDLKVVI 427 Query: 421 LDEPTRGIDVGAKHEIYNVIYQLAERGCAIVMISSELPEVLGVSDRIVVMRQGRISGELT 480 LDEPTRGIDVGAKHEIYNVIYQLAERGCAIVMISSELPEVLGVSDRIVVMRQGRI+GEL+ Sbjct: 428 LDEPTRGIDVGAKHEIYNVIYQLAERGCAIVMISSELPEVLGVSDRIVVMRQGRIAGELS 487 Query: 481 RKDATEQSVLSLALPQSSTALPGTQAAAQQAA 512 RKDATEQ+VLSLALPQSSTALP T AAQQAA Sbjct: 488 RKDATEQAVLSLALPQSSTALPATGTAAQQAA 519 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: 997 Number of extensions: 25 Number of successful extensions: 5 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: 519 Length adjustment: 35 Effective length of query: 477 Effective length of database: 484 Effective search space: 230868 Effective search space used: 230868 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