Align Inositol transport system ATP-binding protein (characterized)
to candidate AO356_20250 AO356_20250 L-arabinose transporter ATP-binding protein
Query= reanno::WCS417:GFF2332 (517 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_20250 Length = 514 Score = 402 bits (1034), Expect = e-116 Identities = 210/489 (42%), Positives = 319/489 (65%), Gaps = 3/489 (0%) Query: 24 LEIVNISKGFPGVVALADVQLRVRPGTVLALMGENGAGKSTLMKIIAGIYQPDAGEIRLR 83 L I K FPGV ALA++ PG V ALMGENGAGKSTL+KI+ G Y P +G++++ Sbjct: 16 LRFNGIGKSFPGVQALANISFVAHPGQVHALMGENGAGKSTLLKILGGAYIPSSGDLQIG 75 Query: 84 GKPIVFETPLAAQKAGIAMIHQELNLMPHMSIAENIWIGREQLNSLHMVNHREMHRCTAE 143 + + F+ + +G+A+IHQEL+L+P M++AEN+++G +VN + + Sbjct: 76 EQTMAFKGTADSIASGVAVIHQELHLVPEMTVAENLFLGHLPAR-FGLVNRGVLRQQALT 134 Query: 144 LLARLRINLDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITEKEVAHLFSII 203 LL L +DP+E+VG LS+ +RQ+VEIAKA+S + ++ DEPTS+++ +E+ L +II Sbjct: 135 LLKGLADEIDPQEKVGRLSLGQRQLVEIAKALSRGAHVIAFDEPTSSLSAREIDRLMAII 194 Query: 204 ADLKSQGKGIVYITHKMNEVFAIADEVAVFRDGHYIG-LQRADSMNSDSLISMMVGRELS 262 A L+ +GK ++Y++H+M EVF I + V VF+DG Y+ + + D L++ MVGR++ Sbjct: 195 ARLRDEGKVVLYVSHRMEEVFRICNAVTVFKDGRYVRTFENMSELTHDQLVTCMVGRDIQ 254 Query: 263 QLFPLRETPIGDLLLTVRDLTLDGVFKDVSFDLHAGEILGIAGLMGSGRTNVAETIFGIT 322 ++ R GD+ L V+ L G+ + VSF +H GEILG+ GL+G+GRT + + G+ Sbjct: 255 DIYDYRPRERGDVALQVKSLLGPGLREPVSFQVHKGEILGLFGLVGAGRTELFRLLSGLE 314 Query: 323 PSSSGQITLDGKAVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENMEMAVLPHYTGN 382 S G + L GK +++ P AI G L EDRK G+ P SV EN+ ++ P ++ Sbjct: 315 RQSEGSLVLHGKELKLRSPRDAIAAGVLLCPEDRKKEGIIPLGSVGENINISARPAHSAL 374 Query: 383 G-FIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLMTNPRLLILDEP 441 G ++ R + K L+VKTP+ Q I LSGGNQQKA+L RWL ++L+LDEP Sbjct: 375 GCLLRGDWERGNADKQIKSLKVKTPAASQKIMYLSGGNQQKAILGRWLSMPMKVLLLDEP 434 Query: 442 TRGIDVGAKAEIYRLIAFLASEGMAVIMISSELPEVLGMSDRVMVMHEGELMGTLDRSEA 501 TRGID+GAKAEIY++I LA++G+AVI++SS+L EV+G+SDR++V+ EG + G L R +A Sbjct: 435 TRGIDIGAKAEIYQIIHNLAADGIAVIVVSSDLMEVMGISDRILVLCEGAMRGELSRDQA 494 Query: 502 TQEKVMQLA 510 + ++QLA Sbjct: 495 NESNLLQLA 503 Score = 81.3 bits (199), Expect = 8e-20 Identities = 57/225 (25%), Positives = 109/225 (48%), Gaps = 6/225 (2%) Query: 42 VQLRVRPGTVLALMGENGAGKSTLMKIIAGIYQPDAGEIRLRGKPIVFETPLAAQKAGIA 101 V +V G +L L G GAG++ L ++++G+ + G + L GK + +P A AG+ Sbjct: 283 VSFQVHKGEILGLFGLVGAGRTELFRLLSGLERQSEGSLVLHGKELKLRSPRDAIAAGVL 342 Query: 102 MIHQELN---LMPHMSIAENIWIGREQLNS-LHMVNHREMHRCTAEL-LARLRINLDPEE 156 + ++ ++P S+ ENI I +S L + + R A+ + L++ Sbjct: 343 LCPEDRKKEGIIPLGSVGENINISARPAHSALGCLLRGDWERGNADKQIKSLKVKTPAAS 402 Query: 157 Q-VGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITEKEVAHLFSIIADLKSQGKGIVY 215 Q + LS +Q + + +S +L++DEPT I A ++ II +L + G ++ Sbjct: 403 QKIMYLSGGNQQKAILGRWLSMPMKVLLLDEPTRGIDIGAKAEIYQIIHNLAADGIAVIV 462 Query: 216 ITHKMNEVFAIADEVAVFRDGHYIGLQRADSMNSDSLISMMVGRE 260 ++ + EV I+D + V +G G D N +L+ + + R+ Sbjct: 463 VSSDLMEVMGISDRILVLCEGAMRGELSRDQANESNLLQLALPRQ 507 Lambda K H 0.320 0.136 0.381 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: 631 Number of extensions: 26 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: 517 Length of database: 514 Length adjustment: 35 Effective length of query: 482 Effective length of database: 479 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 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