Align Arabinose import ATP-binding protein AraG; EC 7.5.2.12 (characterized, see rationale)
to candidate 8502321 DvMF_3029 ABC transporter related (RefSeq)
Query= uniprot:B2SYR5 (512 letters) >FitnessBrowser__Miya:8502321 Length = 537 Score = 264 bits (675), Expect = 5e-75 Identities = 158/493 (32%), Positives = 268/493 (54%), Gaps = 12/493 (2%) Query: 5 LRFDNIGKVFPGVRALDGVSFDVNVGQVHGLMGENGAGKSTLLKILGGEYQPDSGRVMID 64 +R D I K F VRA ++ D+ G + L+GENGAGKSTL+ IL G+ + D+G +++D Sbjct: 30 VRLDGICKSFGKVRANHDITLDIRPGCIKALLGENGAGKSTLMSILAGKLRQDAGTIVVD 89 Query: 65 GNEVRFTSAASSIAAGIAVIHQELQYVPDLTVAENLLLGQLPNSLGWVNKREAKRFVRER 124 G F S ++ AGI +++Q V +TVAEN+LLGQ P+ L + + V Sbjct: 90 GVPTVFASPRDALRAGIGMVYQHFMLVDSMTVAENVLLGQSPDML--LRPARMRDEVAAL 147 Query: 125 LEAMGVALDPNAKLRKLSIAQRQMVEICKALLRNARVIALDEPTSSLSHRETEVLFKLVR 184 E G+A+DP A++ LS+ +RQ VEI K L R++RV+ LDEPT+ L+ RET+ LF+ + Sbjct: 148 AERYGLAVDPAARVGGLSMGERQRVEILKLLYRDSRVLILDEPTAVLTPRETDQLFEAMW 207 Query: 185 DLRADNRAMIYISHRMDEIYELCDACTIFRDGRKIASHPTLEGVTRDTIVSEMVGREISD 244 + +A+++ISH++ E+ + D I R G + + + + + MVGR++ Sbjct: 208 RMADQGKALVFISHKLQEVLTVADEIAILRRGEVVDEFSEADVPNQTVLANRMVGRDV-- 265 Query: 245 IYNYSARPLGEVR--FAAKGIEGHALAQPASFEVRRGEIVGFFGLVGAGRSELMHLVYGA 302 + A+ L V + + + G L+ S +VRRGEIV G+ G G+ EL+ + G Sbjct: 266 VLQVDAKRLTPVDTVLSVEHLSGAGLSD-VSLQVRRGEIVAIAGVAGNGQKELVEAICGL 324 Query: 303 DHKKGGELLLDGKPIKVRSAGEAIRHGIVLCPEDRKEEGIVAMATVSENINISCRRHYLR 362 + GE+ + G+P + AG R G+ PEDR+ + +N ++ R + + Sbjct: 325 ARPEAGEVRILGRPWREFFAGPPGRRGLAYIPEDRQGLATCRHLDLVDNFLLTTRNQFAK 384 Query: 363 VGMFLDRKKEAETADRFIKLLKIKTPSRRQKIRFLSGGNQQKAILSR-WLAEPDLKVVIL 421 G+FLDR + R + ++ R LSGGN QK ++ R + +P+ V++ Sbjct: 385 -GVFLDRTEATNAVKRVVWEYNVQPGDITAPARALSGGNLQKLVIGREFFRKPE--VIVA 441 Query: 422 DEPTRGIDVGAKHEIYNVIYQLAERGCAIVMISSELPEVLGVSDRIVVMRQGRISGELTR 481 + PT+G+D+ A E++ + + A +++++ +L E L ++DRI VM +GR + Sbjct: 442 ENPTQGLDISATEEVWGRLLE-ARSTSGVLLVTGDLNEALELADRIAVMYRGRFIDVFDK 500 Query: 482 KDATEQSVLSLAL 494 D + + L + Sbjct: 501 DDTAKVQAIGLMM 513 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: 605 Number of extensions: 39 Number of successful extensions: 8 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: 537 Length adjustment: 35 Effective length of query: 477 Effective length of database: 502 Effective search space: 239454 Effective search space used: 239454 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