Align Arabinose import ATP-binding protein AraG; EC 7.5.2.12 (characterized, see rationale)
to candidate 3607108 Dshi_0530 ABC transporter related (RefSeq)
Query= uniprot:B2SYR5 (512 letters) >FitnessBrowser__Dino:3607108 Length = 498 Score = 287 bits (735), Expect = 5e-82 Identities = 166/481 (34%), Positives = 270/481 (56%), Gaps = 4/481 (0%) Query: 10 IGKVFPGVRALDGVSFDVNVGQVHGLMGENGAGKSTLLKILGGEYQPDSGRVMIDGNEVR 69 I K + GV ALD V F V G+ L GENG+GKSTL+KI+ G +G V I G E Sbjct: 15 ITKRYAGVTALDSVDFTVQPGEAVCLAGENGSGKSTLIKIISGVEPATAGTVQIAGQEHV 74 Query: 70 FTSAASSIAAGIAVIHQELQYVPDLTVAENLLLG-QLPNSLGWVNKREAKRFVRERLEAM 128 + S AAG+ VI Q+ P+L+VAEN+ QL R + R L+ + Sbjct: 75 TLNPRISAAAGVMVIFQDFSLFPNLSVAENIAFTTQLSTRQRLFKFRAVRDIARAALDRI 134 Query: 129 GVALDPNAKLRKLSIAQRQMVEICKALLRNARVIALDEPTSSLSHRETEVLFKLVRDLRA 188 GV +D +A++ L +AQ+Q+V IC+AL A++I +DEPT++L+ +E L ++R L+ Sbjct: 135 GVQIDLDARVETLPVAQKQLVAICRALASKAQLIIMDEPTTALTEKEVRRLQGIIRMLKE 194 Query: 189 DNRAMIYISHRMDEIYELCDACTIFRDGRKIASHPTLEGVTRDTIVSEMVGREISDIYNY 248 + A+I++SH++ E+ E+ + + R+G+K+A P E T+ ++ M GR++ ++ Sbjct: 195 EGVAVIFVSHKLAEVLEVSEKVVVLRNGKKVAEGPASEFDTQ-SLTYHMTGRDVPEVPPS 253 Query: 249 SARPLGEVRFAAKGIEGHALAQPASFEVRRGEIVGFFGLVGAGRSELMHLVYGADHKKGG 308 + +G+ SF++R GE++G GL+G GR+ + ++G G Sbjct: 254 DVAAGAQTLMQVQGLGKAGSFSDISFDLRTGEVLGITGLLGCGRTSVAKALFGLVTPDAG 313 Query: 309 ELLLDGKPIKVRSAGEAIRHGIVLCPEDRKEEGIVAMATVSENINISCRRHYLRVGMFLD 368 +L+DG P+ + A I PEDR EG+ ++ N+ + R G FLD Sbjct: 314 SILVDGSPVPLGDPQAASLARIGYVPEDRLTEGLFLSQSILRNVAVG-RLDAHTSGGFLD 372 Query: 369 RKKEAETADRFIKLLKIKTPSRRQKIRFLSGGNQQKAILSRWLAEPDLKVVILDEPTRGI 428 A+ A +++ LK+K P ++ LSGGNQQ+ L+RWL+ +V+IL+ P+ G+ Sbjct: 373 MTGLAKEASDWLRRLKVKAPDVEAPVQSLSGGNQQRVALARWLSRAP-RVLILNGPSVGV 431 Query: 429 DVGAKHEIYNVIYQLAERGCAIVMISSELPEVLGVSDRIVVMRQGRISGELTRKDATEQS 488 DVG+K +I+++I +LA G +++IS +LPE+L R++VMR+GRI L TE Sbjct: 432 DVGSKADIHDIIRELAREGIGVIVISDDLPELLATCHRVLVMREGRIIDALEGTALTEDD 491 Query: 489 V 489 + Sbjct: 492 L 492 Score = 64.7 bits (156), Expect = 7e-15 Identities = 60/258 (23%), Positives = 112/258 (43%), Gaps = 15/258 (5%) Query: 255 EVRFAAKGIEGHALAQPASFEVRRGEIVGFFGLVGAGRSELMHLVYGADHKKGGELLLDG 314 ++R K G F V+ GE V G G+G+S L+ ++ G + G + + G Sbjct: 11 DLRAITKRYAGVTALDSVDFTVQPGEAVCLAGENGSGKSTLIKIISGVEPATAGTVQIAG 70 Query: 315 KPIKVRSAGEAIRHGIVLCPEDRKEEGIVAMATVSENI----NISCRRHYLRVGMFLDRK 370 + + + G+++ +D + +V+ENI +S R+ + D Sbjct: 71 QEHVTLNPRISAAAGVMVIFQDFS---LFPNLSVAENIAFTTQLSTRQRLFKFRAVRDIA 127 Query: 371 KEAETADRFIKLLKIKTPSRRQKIRFLSGGNQQKAILSRWLAEPDLKVVILDEPTRGIDV 430 + A DR + + ++ L +Q + R LA +++I+DEPT + Sbjct: 128 RAA--LDRIGVQIDLDA-----RVETLPVAQKQLVAICRALASK-AQLIIMDEPTTALTE 179 Query: 431 GAKHEIYNVIYQLAERGCAIVMISSELPEVLGVSDRIVVMRQGRISGELTRKDATEQSVL 490 + +I L E G A++ +S +L EVL VS+++VV+R G+ E + QS+ Sbjct: 180 KEVRRLQGIIRMLKEEGVAVIFVSHKLAEVLEVSEKVVVLRNGKKVAEGPASEFDTQSLT 239 Query: 491 SLALPQSSTALPGTQAAA 508 + +P + AA Sbjct: 240 YHMTGRDVPEVPPSDVAA 257 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: 578 Number of extensions: 31 Number of successful extensions: 8 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: 498 Length adjustment: 34 Effective length of query: 478 Effective length of database: 464 Effective search space: 221792 Effective search space used: 221792 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