Align Arabinose import ATP-binding protein AraG; EC 7.5.2.12 (characterized, see rationale)
to candidate WP_101446908.1 BD749_RS17540 gliding motility-associated ABC transporter ATP-binding subunit GldA
Query= uniprot:B2SYR5 (512 letters) >NCBI__GCF_002846395.1:WP_101446908.1 Length = 303 Score = 107 bits (267), Expect = 6e-28 Identities = 71/212 (33%), Positives = 110/212 (51%), Gaps = 6/212 (2%) Query: 9 NIGKVFPGVRALDGVSFDVNVGQVHGLMGENGAGKSTLLKILGGEYQPDSGRVMIDGNEV 68 N+ K+F RA+D +SF V+ GQ+ G +G NGAGKST +KI P +G V++ G +V Sbjct: 7 NLTKLFGSQRAVDDISFSVSQGQILGFLGPNGAGKSTTMKIATCYLPPSAGTVLVAGYDV 66 Query: 69 RFTSAASSIAAGIAVIHQELQYVPDLTVAENLLLGQLPNSLGWVNKREAKRFVRERLEAM 128 A G H L D+ V E L Q S+ + R AK V E +E Sbjct: 67 LQDPIAVRRNVGYLPEHNPLYL--DMYVHEYL---QFVASVYGLKGRLAKERVHEMVELC 121 Query: 129 GVALDPNAKLRKLSIAQRQMVEICKALLRNARVIALDEPTSSLSHRETEVLFKLVRDLRA 188 G+ L+ K+ LS RQ V + +AL+ + +V+ LDEPT+ L + + L++ + Sbjct: 122 GLTLEQGKKIGALSKGYRQRVGLAQALVHDPQVLILDEPTTGLDPNQIVEIRSLIKRIGQ 181 Query: 189 DNRAMIYISHRMDEIYELCDACTIFRDGRKIA 220 D + +I+ +H M E+ +CD I G+ +A Sbjct: 182 D-KTVIFSTHIMQEVTAICDRVVIINRGKLVA 212 Score = 58.5 bits (140), Expect = 3e-13 Identities = 58/221 (26%), Positives = 102/221 (46%), Gaps = 14/221 (6%) Query: 255 EVRFAAKGIEGHALAQPASFEVRRGEIVGFFGLVGAGRSELMHLVYGADHKKGGELLLDG 314 EV+ K SF V +G+I+GF G GAG+S M + G +L+ G Sbjct: 4 EVKNLTKLFGSQRAVDDISFSVSQGQILGFLGPNGAGKSTTMKIATCYLPPSAGTVLVAG 63 Query: 315 KPIKVRSAGEAIRHGIVLCPEDRKEEGIVAMATVSENINISCRRHYLRVGMFLDRKKEAE 374 V A+R + PE + V E + + L+ + +R E Sbjct: 64 --YDVLQDPIAVRRNVGYLPE---HNPLYLDMYVHEYLQFVASVYGLKGRLAKERVHE-- 116 Query: 375 TADRFIKLLKIKTPSRRQKIRFLSGGNQQKAILSRWLAEPDLKVVILDEPTRGIDVGAKH 434 ++L + T + +KI LS G +Q+ L++ L D +V+ILDEPT G+D Sbjct: 117 ----MVELCGL-TLEQGKKIGALSKGYRQRVGLAQALVH-DPQVLILDEPTTGLDPNQIV 170 Query: 435 EIYNVIYQLAERGCAIVMISSELPEVLGVSDRIVVMRQGRI 475 EI ++I ++ + ++ + + EV + DR+V++ +G++ Sbjct: 171 EIRSLIKRIGQ-DKTVIFSTHIMQEVTAICDRVVIINRGKL 210 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: 289 Number of extensions: 17 Number of successful extensions: 4 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: 303 Length adjustment: 31 Effective length of query: 481 Effective length of database: 272 Effective search space: 130832 Effective search space used: 130832 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: 50 (23.9 bits)
This GapMind analysis is from Sep 24 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