Align Arabinose import ATP-binding protein AraG; EC 7.5.2.12 (characterized, see rationale)
to candidate WP_084931811.1 HA51_RS03115 sugar ABC transporter ATP-binding protein
Query= uniprot:A0A165ZSX8 (514 letters) >NCBI__GCF_002095475.1:WP_084931811.1 Length = 504 Score = 381 bits (978), Expect = e-110 Identities = 206/501 (41%), Positives = 314/501 (62%), Gaps = 6/501 (1%) Query: 16 LRFNGIGKSFPGVQALANISFVAHPGQVHALMGENGAGKSTLLKILGGAYIPSSGDLQIG 75 + I K+F G+ AL G+VHAL+GENGAGKSTL+++LGG + P SG + Sbjct: 6 IELRDIVKTFGGIHALKGAQLQIRAGEVHALLGENGAGKSTLMRVLGGEHTPDSGTVYDK 65 Query: 76 EQTMAFKGTADSIASGVAVIHQELHLVPEMTVAENLFLGHLPARFGLVNRGVLRQQALTL 135 + + KG ++A G+ +IHQE+ L E+TVAEN+FL LP + LR +A + Sbjct: 66 GEAVQIKGPKAAMARGITLIHQEMALAQELTVAENIFLHDLPT---FIAWPKLRAKAANI 122 Query: 136 LKGLADEIDPQEKVGRLSLGQRQLVEIAKALSRGAHVIAFDEPTSSLSAREIDRLMAIIG 195 L+ L EIDP VG LS+ +Q+VEIA+ALS+ A VI FDEPT+ LS ++ +RL+ II Sbjct: 123 LRRLGFEIDPAATVGDLSVAHQQIVEIARALSQDARVIVFDEPTAVLSTQDANRLLEIIS 182 Query: 196 RLRDEGKVVLYVSHRMEEVFRICNAVTVFKDGRYVRTFENMSELTHDQLVTCMVGRDIQD 255 LR G ++Y+SHR++EVFRI + +T+ KDG+++ T E+ + T +++ MVGR + Sbjct: 183 DLRSVGVAIVYISHRLDEVFRIADRMTIMKDGQWIAT-ESPQQTTLQEVIRLMVGRPVDQ 241 Query: 256 IYDYRPRE-RGDVALQVKGLLGPGLHEPVSFQVHKGEILGLFGLVGAGRTELLRLLSGLE 314 ++ R G+ L+V+ L VSF V GE++GL GLVG+GRTE+ RL+ G + Sbjct: 242 LFSDRATYGMGEEVLRVEKLNARRKVRDVSFSVRAGEVVGLGGLVGSGRTEVARLIFGAD 301 Query: 315 RQREGSLVLHDKELKLRSPRDAIAAGVLLCPEDRKKEGIIPLGSVGENINISARPSHSTL 374 R G + LH K++ LRSP+ A+ AG+ L PEDRK++G++ + N+ ++ + Sbjct: 302 RCDSGDIYLHGKKVSLRSPQQAVKAGIALVPEDRKRQGVVLDMPIRANVTMANDKAVMAP 361 Query: 375 GCLLRGDWERGNADKQIKSLKVKTPTAGQKIMYLSGGNQQKAILGRWLSMPMKVLLLDEP 434 + E K + +++K + LSGGNQQK +L +W ++ +V++LDEP Sbjct: 362 LGFIHSSRETQVVSKLAQQMRLKCAGLHAPVSSLSGGNQQKVVLAKWFNLGGQVIILDEP 421 Query: 435 TRGIDIGAKAEIYQIIHNLAADGIAVIVVSSDLMEVMGISDRILVLCEGAMRGELSRDQA 494 TRG+D+GAK EIYQ+I LA G+AV+V+SS+ +E+ G+ +R+LV+ EGA+ GEL D Sbjct: 422 TRGVDVGAKREIYQLIAELAQQGMAVVVISSEHIELFGLCNRVLVMSEGAICGELQPDDY 481 Query: 495 NESNLLQLALP-RQRVADAAN 514 +E NLL +A+ R ++ A N Sbjct: 482 SEENLLSMAMTHRSSLSHAEN 502 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: 644 Number of extensions: 30 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: 504 Length adjustment: 34 Effective length of query: 480 Effective length of database: 470 Effective search space: 225600 Effective search space used: 225600 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 24 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