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) >FitnessBrowser__Dino:3609044 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:
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