Align Arabinose import ATP-binding protein AraG; EC 7.5.2.12 (characterized, see rationale)
to candidate 3609044 Dshi_2433 ABC transporter related (RefSeq)
Query= uniprot:B2SYR5 (512 letters) >lcl|FitnessBrowser__Dino:3609044 Dshi_2433 ABC transporter related (RefSeq) Length = 510 Score = 376 bits (966), Expect = e-109 Identities = 198/489 (40%), Positives = 305/489 (62%), Gaps = 4/489 (0%) Query: 3 ATLRFDNIGKVFPGVRALDGVSFDVNVGQVHGLMGENGAGKSTLLKILGGEYQPDSGRVM 62 A L +I K FPGV+AL VS + G+V L+GENGAGKST++KIL G YQPD GR++ Sbjct: 19 AALALAHITKTFPGVKALSDVSLSLYPGKVTALIGENGAGKSTVVKILTGIYQPDGGRIL 78 Query: 63 IDGNEVRFTSAASSIAAGIAVIHQELQYVPDLTVAENLLLGQLP-NSLGWVNKREAKRFV 121 +DG V F++ ++ G+ IHQE +L+VAEN+ LG P + G ++ ++ Sbjct: 79 VDGQPVPFSTPQAAADHGVTAIHQETVLFDELSVAENIFLGHAPRGAFGLIDWKKTTENA 138 Query: 122 RERLEAMGVALDPNAKLRKLSIAQRQMVEICKALLRNARVIALDEPTSSLSHRETEVLFK 181 R L ++G LDP+ KL+ L IA + +V I +AL ARV+ +DEPT++LSH+E E L++ Sbjct: 139 RALLTSIGAELDPDHKLKDLGIANKHLVAIARALSIEARVVIMDEPTAALSHKEIEELYE 198 Query: 182 LVRDLRADNRAMIYISHRMDEIYELCDACTIFRDGRKIASHPTLEGVTRDTIVSEMVGRE 241 LV L+A +A+++ISH+ DEI+ + D T+FRDG+ I + VT +V MVGR+ Sbjct: 199 LVESLKAQGKAILFISHKFDEIFRIADNYTVFRDGQLIGD-GAIADVTEADLVKMMVGRD 257 Query: 242 ISDIYNYSARPLGEVRFAAKGIEGHALAQPASFEVRRGEIVGFFGLVGAGRSELMHLVYG 301 +S I+ A +G+ +G SF +R GEI+GF+GLVGAGRSE M ++G Sbjct: 258 VSQIFPQRAPNVGDTVLTVQGYAHPTEFDDISFTLREGEILGFYGLVGAGRSEFMQSLFG 317 Query: 302 ADHKKGGELLLDGKPIKVRSAGEAIRHGIVLCPEDRKEEGIVAMATVSENINISCRRHYL 361 G + + G ++ S +A+ HGIV PEDR ++G + + +N+ + Sbjct: 318 ITRPSAGSVEIGGARAEISSPADAVDHGIVYVPEDRGKQGAILDLPIFQNVTLPSLGRIS 377 Query: 362 RVGMFLDRKKEAETADRFIKLLKIKTPSRRQKIRFLSGGNQQKAILSRWLAEPDLKVVIL 421 R G FL +E A + + L ++ S + LSGGNQQK ++++WLA +V+IL Sbjct: 378 RKG-FLRLAEEFALAREYTERLDLRAASLDTHVGNLSGGNQQKVVIAKWLATRP-RVIIL 435 Query: 422 DEPTRGIDVGAKHEIYNVIYQLAERGCAIVMISSELPEVLGVSDRIVVMRQGRISGELTR 481 DEPT+G+D+G+K +++ + +LA +G A++M+SSE+PEVLG+SDR++VMR+GRI EL Sbjct: 436 DEPTKGVDIGSKAAVHDFMAELAAQGLAVIMVSSEIPEVLGMSDRVIVMREGRIVAELAG 495 Query: 482 KDATEQSVL 490 D ++++ Sbjct: 496 DDLQPETLV 504 Score = 80.9 bits (198), Expect = 1e-19 Identities = 62/234 (26%), Positives = 110/234 (47%), Gaps = 11/234 (4%) Query: 261 KGIEGHALAQPASFEVRRGEIVGFFGLVGAGRSELMHLVYGADHKKGGELLLDGKPIKVR 320 K G S + G++ G GAG+S ++ ++ G GG +L+DG+P+ Sbjct: 28 KTFPGVKALSDVSLSLYPGKVTALIGENGAGKSTVVKILTGIYQPDGGRILVDGQPVPFS 87 Query: 321 SAGEAIRHGIVLCPEDRKEEGIVAMATVSENINISCRRHYLRVGMF--LDRKKEAETADR 378 + A HG+ +E + +V+ENI + H R G F +D KK E A Sbjct: 88 TPQAAADHGVTAI---HQETVLFDELSVAENIFLG---HAPR-GAFGLIDWKKTTENARA 140 Query: 379 FIKLLKIKTPSRRQKIRFLSGGNQQKAILSRWLAEPDLKVVILDEPTRGIDVGAKHEIYN 438 + + + K++ L N+ ++R L+ + +VVI+DEPT + E+Y Sbjct: 141 LLTSIGAELDPDH-KLKDLGIANKHLVAIARALSI-EARVVIMDEPTAALSHKEIEELYE 198 Query: 439 VIYQLAERGCAIVMISSELPEVLGVSDRIVVMRQGRISGELTRKDATEQSVLSL 492 ++ L +G AI+ IS + E+ ++D V R G++ G+ D TE ++ + Sbjct: 199 LVESLKAQGKAILFISHKFDEIFRIADNYTVFRDGQLIGDGAIADVTEADLVKM 252 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: 673 Number of extensions: 38 Number of successful extensions: 9 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: 510 Length adjustment: 35 Effective length of query: 477 Effective length of database: 475 Effective search space: 226575 Effective search space used: 226575 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.
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