Align Arabinose import ATP-binding protein AraG; EC 7.5.2.12 (characterized, see rationale)
to candidate 3607097 Dshi_0519 ABC transporter related (RefSeq)
Query= uniprot:A0A165ZSX8 (514 letters) >FitnessBrowser__Dino:3607097 Length = 498 Score = 291 bits (744), Expect = 5e-83 Identities = 174/474 (36%), Positives = 264/474 (55%), Gaps = 8/474 (1%) Query: 19 NGIGKSFPGVQALANISFVAHPGQVHALMGENGAGKSTLLKILGGAYIPSSGDLQIGEQT 78 NG+ KSF L I PG V LMG NGAGKSTL+K++ G + G +++ Sbjct: 2 NGLQKSFGKNNVLRGIDLTLDPGSVTVLMGANGAGKSTLVKVICGQHRADGGTMRLATNA 61 Query: 79 MAFKGTADSIASGVAVIHQELH--LVPEMTVAENLFLGHLPAR-FGL-VNRGVLRQQALT 134 + AD+I GV +HQ + ++P++ VA NL L L GL V LR +A Sbjct: 62 FDPEDAADAIRQGVVTVHQSIDDGVIPDLDVANNLMLDRLAEHSHGLFVRERHLRTEAAK 121 Query: 135 LLKGLADEIDPQEKVGRLSLGQRQLVEIAKALSRGAHVIAFDEPTSSLSAREIDRLMAII 194 + + E++ + +V LS+ RQ++ IA+A++R V+ DEPTSSLSA E DRL +I Sbjct: 122 VAAAMGIEVNLRARVSDLSVADRQMIAIARAMARAPKVLILDEPTSSLSATEADRLFELI 181 Query: 195 GRLRDEGKVVLYVSHRMEEVFRICNAVTVFKDGRYVRTFENMSELTHDQLVTCMVGRDIQ 254 RLR +G +LY+SHRM ++ RI + + V +DG FE L + VT M+G + Sbjct: 182 DRLRAQGVAILYISHRMSDIRRIADRIVVMRDGMISGVFET-EPLDLEAAVTAMLGHRMT 240 Query: 255 DIYDYRPRERGDVALQVKGLLGPGLHEPVSFQVHKGEILGLFGLVGAGRTELLRLLSGLE 314 ++ D R+ L++K L P++ H GE++ L GL+G+G++ L +L G+ Sbjct: 241 EV-DAEVRQGTHPVLEIKNLQLFEGASPITLTAHDGEVVALVGLLGSGKSRLAEILFGIA 299 Query: 315 RQREGSLVLHDKELKLRSPRDAIAAGVLLCPEDRKKEGIIPLGSVGENINISARPSHSTL 374 R GS+ + K+ RS +DAIA GV + P+DR +IP + +N+ + S + Sbjct: 300 RPIRGSIRIKGKDYSPRSVKDAIAQGVFMSPKDRGTNAVIPAFDIADNMTLPFLQGMS-V 358 Query: 375 GCLLRGDWERGNADKQIKSLKVKTPTAGQKIMYLSGGNQQKAILGRWLSMPMKVLLLDEP 434 G L+ +RG A + L + + I LSGGNQQK ++ RWL P +VLLLDEP Sbjct: 359 GSFLKSRQQRGTAQGMVDRLGIVCQSVRDGIGTLSGGNQQKVMIARWLLEPAQVLLLDEP 418 Query: 435 TRGIDIGAKAEIYQIIHNLAADGIAVIVVSSDLMEVMGISDRILVLCEGAMRGE 488 +G+DIGA+ +I I G A +V +++ E + I+DRI+V+ EGA+ GE Sbjct: 419 FQGVDIGARRDIGHHI-RATTQGRATLVFLAEIDEALEIADRIVVMSEGAIVGE 471 Lambda K H 0.320 0.138 0.391 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: 624 Number of extensions: 46 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: 514 Length of database: 498 Length adjustment: 34 Effective length of query: 480 Effective length of database: 464 Effective search space: 222720 Effective search space used: 222720 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