Align L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 (characterized)
to candidate 8502321 DvMF_3029 ABC transporter related (RefSeq)
Query= CharProtDB::CH_014279 (504 letters) >FitnessBrowser__Miya:8502321 Length = 537 Score = 245 bits (625), Expect = 3e-69 Identities = 160/501 (31%), Positives = 264/501 (52%), Gaps = 19/501 (3%) Query: 6 PYLSFRGIGKTFPGVKALTDISFDCYAGQVHALMGENGAGKSTLLKILSGNYAPTTGSVV 65 P + GI K+F V+A DI+ D G + AL+GENGAGKSTL+ IL+G G++V Sbjct: 28 PVVRLDGICKSFGKVRANHDITLDIRPGCIKALLGENGAGKSTLMSILAGKLRQDAGTIV 87 Query: 66 INGQEMSFSDTTAALNAGVAIIYQELHLVPEMTVAENIYLGQLPHKGGIVNRSLLNYEAG 125 ++G F+ AL AG+ ++YQ LV MTVAEN+ LGQ P ++ + + E Sbjct: 88 VDGVPTVFASPRDALRAGIGMVYQHFMLVDSMTVAENVLLGQSPDM--LLRPARMRDEVA 145 Query: 126 LQLKHLGMDIDPDTPLKYLSIGQWQMVEIAKALARNAKIIAFDEPTSSLSAREIDNLFRV 185 + G+ +DP + LS+G+ Q VEI K L R+++++ DEPT+ L+ RE D LF Sbjct: 146 ALAERYGLAVDPAARVGGLSMGERQRVEILKLLYRDSRVLILDEPTAVLTPRETDQLFEA 205 Query: 186 IRELRKEGRVILYVSHRMEEIFALSDAITVFKDGRYVKTFTDMQQVDHDALVQAMVGRDI 245 + + +G+ ++++SH+++E+ ++D I + + G V F++ + L MVGRD+ Sbjct: 206 MWRMADQGKALVFISHKLQEVLTVADEIAILRRGEVVDEFSEADVPNQTVLANRMVGRDV 265 Query: 246 GDIYGWQPRSYGEERLRLDAVKAPGVRTPISLAVRSGEIVGLFGLVGAGRSELMKGMFGG 305 + + + L ++ + G+ + +SL VR GEIV + G+ G G+ EL++ + G Sbjct: 266 VLQVDAKRLTPVDTVLSVEHLSGAGL-SDVSLQVRRGEIVAIAGVAGNGQKELVEAICGL 324 Query: 306 TQITAGQVYIDQQPIDIRKPSHAIAAGMMLCPEDRKAEGIIPVHSVRDNINISARRKHVL 365 + AG+V I +P G+ PEDR+ + DN ++ R + Sbjct: 325 ARPEAGEVRILGRPWREFFAGPPGRRGLAYIPEDRQGLATCRHLDLVDNFLLTTRNQFAK 384 Query: 366 GGCVINNGWEENNA------DHHIRSLNIKTPGAEQLIMNLSGGNQQKAILGRWLSEEMK 419 G V + E NA +++++ +I P LSGGN QK ++GR + + Sbjct: 385 G--VFLDRTEATNAVKRVVWEYNVQPGDITAPARA-----LSGGNLQKLVIGREFFRKPE 437 Query: 420 VILLDEPTRGIDVGAKHEIY-NVIYALAAQGVAVLFASSDLPEVLGVADRIVVMREGEIA 478 VI+ + PT+G+D+ A E++ ++ A + G VL + DL E L +ADRI VM G Sbjct: 438 VIVAENPTQGLDISATEEVWGRLLEARSTSG--VLLVTGDLNEALELADRIAVMYRGRFI 495 Query: 479 GELLHEQADERQALSLAMPKV 499 + + QA+ L M V Sbjct: 496 DVFDKDDTAKVQAIGLMMAGV 516 Lambda K H 0.319 0.136 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: 635 Number of extensions: 48 Number of successful extensions: 9 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: 504 Length of database: 537 Length adjustment: 35 Effective length of query: 469 Effective length of database: 502 Effective search space: 235438 Effective search space used: 235438 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 (21.7 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