Align L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 (characterized)
to candidate GFF385 PGA1_c03960 ribose import ATP-binding protein RbsA
Query= CharProtDB::CH_014279 (504 letters) >FitnessBrowser__Phaeo:GFF385 Length = 509 Score = 275 bits (702), Expect = 4e-78 Identities = 179/515 (34%), Positives = 272/515 (52%), Gaps = 21/515 (4%) Query: 4 STPYLSFRGIGKTFPGVKALTDISFDCYAGQVHALMGENGAGKSTLLKILSGNYAPTTGS 63 + P + +GI K F V+A DIS G +H ++GENGAGKSTL+ IL G Y G Sbjct: 2 TAPAIELKGISKAFGPVQANKDISIRVAPGTIHGIIGENGAGKSTLMSILYGFYKADKGE 61 Query: 64 VVINGQEMSFSDTTAALNAGVAIIYQELHLVPEMTVAENIYLGQLPHKGGIVNRSLLNYE 123 V I+G+ D+ AA++AG+ +++Q LV TV ENI LG GG++ SL + Sbjct: 62 VWIHGKRTEIPDSQAAISAGIGMVFQHFKLVENFTVLENIILG--AEDGGLLKPSL--SK 117 Query: 124 AGLQLKHLG----MDIDPDTPLKYLSIGQWQMVEIAKALARNAKIIAFDEPTSSLSAREI 179 A LK L +++DPD + + +G Q VEI KAL R A I+ DEPT L+ E Sbjct: 118 ARKSLKDLAAEYELNVDPDARIDEIGVGMQQRVEILKALYRQADILILDEPTGVLTPAEA 177 Query: 180 DNLFRVIRELRKEGRVILYVSHRMEEIFALSDAITVFKDGRYVKTFTDMQQVDHDALVQA 239 D LFR++ LR EG+ I+ ++H++ EI +D ++V + G T + + L + Sbjct: 178 DQLFRILDRLRAEGKTIILITHKLREIMEYTDTVSVMRRGEMTAT-VKTAETSPEHLAEL 236 Query: 240 MVGRDIGDIYGWQPRSYGEERL---RLDAVKAPGVR--TPISLAVRSGEIVGLFGLVGAG 294 MVGR + P + G+ L L V GV I L VR+GEI+G+ G+ G G Sbjct: 237 MVGRKVLLRVDKVPATPGKPILEIENLSVVDEAGVARVKNIDLTVRAGEILGIAGVAGNG 296 Query: 295 RSELMKGMFGGTQITAGQVYIDQQPIDIRKPSHAI----AAGMMLCPEDRKAEGIIPVHS 350 +SELM+ + GG + G + ++ P+ + AA + PEDR+ EG+I Sbjct: 297 QSELME-VLGGMREGQGSIRLNGAPLPLSGAGSDARARRAAHVAHVPEDRQREGLIMDFH 355 Query: 351 VRDNINISARR-KHVLGGCVINNGWEENNADHHIRSLNIKTPGAEQLIMNLSGGNQQKAI 409 +N+ G ++NN + + + +++ P N SGGNQQK + Sbjct: 356 AWENVAFGYHHAPEYQRGLLMNNAALRADTEAKMAKFDVRPPDPWLAAKNFSGGNQQKIV 415 Query: 410 LGRWLSEEMKVILLDEPTRGIDVGAKHEIYNVIYALAAQGVAVLFASSDLPEVLGVADRI 469 + R + +++L+ +PTRG+D+GA I+ I L QG A+L S +L E+L +ADR+ Sbjct: 416 VAREIERNPELLLIGQPTRGVDIGAIEFIHKQIVELRDQGKAILLVSVELEEILSLADRV 475 Query: 470 VVMREGEIAGELLHEQADERQALSLAMPKVSQAVA 504 VM +G I GE +Q DE++ L L M V+ A Sbjct: 476 AVMFDGMIMGERPADQTDEKE-LGLLMAGVAGEAA 509 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: 630 Number of extensions: 38 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: 509 Length adjustment: 34 Effective length of query: 470 Effective length of database: 475 Effective search space: 223250 Effective search space used: 223250 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