Align Arabinose import ATP-binding protein AraG; EC 7.5.2.12 (characterized, see rationale)
to candidate GFF2332 PS417_11890 D-ribose transporter ATP-binding protein
Query= uniprot:A0A165ZSX8 (514 letters) >FitnessBrowser__WCS417:GFF2332 Length = 517 Score = 396 bits (1018), Expect = e-115 Identities = 208/489 (42%), Positives = 315/489 (64%), Gaps = 3/489 (0%) Query: 16 LRFNGIGKSFPGVQALANISFVAHPGQVHALMGENGAGKSTLLKILGGAYIPSSGDLQIG 75 L I K FPGV ALA++ PG V ALMGENGAGKSTL+KI+ G Y P +G++++ Sbjct: 24 LEIVNISKGFPGVVALADVQLRVRPGTVLALMGENGAGKSTLMKIIAGIYQPDAGEIRLR 83 Query: 76 EQTMAFKGTADSIASGVAVIHQELHLVPEMTVAENLFLGHLPAR-FGLVNRGVLRQQALT 134 + + F+ + +G+A+IHQEL+L+P M++AEN+++G +VN + + Sbjct: 84 GKPIVFETPLAAQKAGIAMIHQELNLMPHMSIAENIWIGREQLNSLHMVNHREMHRCTAE 143 Query: 135 LLKGLADEIDPQEKVGRLSLGQRQLVEIAKALSRGAHVIAFDEPTSSLSAREIDRLMAII 194 LL L +DP+E+VG LS+ +RQ+VEIAKA+S + ++ DEPTS+++ +E+ L +II Sbjct: 144 LLARLRINLDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITEKEVAHLFSII 203 Query: 195 GRLRDEGKVVLYVSHRMEEVFRICNAVTVFKDGRYVRTFENMSELTHDQLVTCMVGRDIQ 254 L+ +GK ++Y++H+M EVF I + V VF+DG Y+ + + D L++ MVGR++ Sbjct: 204 ADLKSQGKGIVYITHKMNEVFAIADEVAVFRDGHYIG-LQRADSMNSDSLISMMVGRELS 262 Query: 255 DIYDYRPRERGDVALQVKGLLGPGLHEPVSFQVHKGEILGLFGLVGAGRTELLRLLSGLE 314 ++ R GD+ L V+ L G+ + VSF +H GEILG+ GL+G+GRT + + G+ Sbjct: 263 QLFPLRETPIGDLLLTVRDLTLDGVFKDVSFDLHAGEILGIAGLMGSGRTNVAETIFGIT 322 Query: 315 RQREGSLVLHDKELKLRSPRDAIAAGVLLCPEDRKKEGIIPLGSVGENINISARPSHSTL 374 G + L K +++ P AI G L EDRK G+ P SV EN+ ++ P H T Sbjct: 323 PSSSGQITLDGKAVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENMEMAVLP-HYTG 381 Query: 375 GCLLRGDWERGNADKQIKSLKVKTPTAGQKIMYLSGGNQQKAILGRWLSMPMKVLLLDEP 434 ++ R + K L+VKTP+ Q I LSGGNQQKA+L RWL ++L+LDEP Sbjct: 382 NGFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLMTNPRLLILDEP 441 Query: 435 TRGIDIGAKAEIYQIIHNLAADGIAVIVVSSDLMEVMGISDRILVLCEGAMRGELSRDQA 494 TRGID+GAKAEIY++I LA++G+AVI++SS+L EV+G+SDR++V+ EG + G L R +A Sbjct: 442 TRGIDVGAKAEIYRLIAFLASEGMAVIMISSELPEVLGMSDRVMVMHEGELMGTLDRSEA 501 Query: 495 NESNLLQLA 503 + ++QLA Sbjct: 502 TQEKVMQLA 510 Score = 79.3 bits (194), Expect = 3e-19 Identities = 59/236 (25%), Positives = 113/236 (47%), Gaps = 6/236 (2%) Query: 272 KGLLGPGLHEPVSFQVHKGEILGLFGLVGAGRTELLRLLSGLERQREGSLVLHDKELKLR 331 KG G V +V G +L L G GAG++ L+++++G+ + G + L K + Sbjct: 31 KGFPGVVALADVQLRVRPGTVLALMGENGAGKSTLMKIIAGIYQPDAGEIRLRGKPIVFE 90 Query: 332 SPRDAIAAGVLLCPEDRKKEGIIPLGSVGENINISARPSHSTLGCLLRGDWERGNADKQI 391 +P A AG+ + ++ ++P S+ ENI I R ++L + + R A+ + Sbjct: 91 TPLAAQKAGIAMIHQELN---LMPHMSIAENIWIG-REQLNSLHMVNHREMHRCTAEL-L 145 Query: 392 KSLKVKTPTAGQKIMYLSGGNQQKAILGRWLSMPMKVLLLDEPTRGIDIGAKAEIYQIIH 451 L++ Q + LS +Q + + +S +L++DEPT I A ++ II Sbjct: 146 ARLRINLDPEEQ-VGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITEKEVAHLFSIIA 204 Query: 452 NLAADGIAVIVVSSDLMEVMGISDRILVLCEGAMRGELSRDQANESNLLQLALPRQ 507 +L + G ++ ++ + EV I+D + V +G G D N +L+ + + R+ Sbjct: 205 DLKSQGKGIVYITHKMNEVFAIADEVAVFRDGHYIGLQRADSMNSDSLISMMVGRE 260 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: 665 Number of extensions: 30 Number of successful extensions: 9 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 2 Length of query: 514 Length of database: 517 Length adjustment: 35 Effective length of query: 479 Effective length of database: 482 Effective search space: 230878 Effective search space used: 230878 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 Apr 09 2024. 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