Align AraV, component of Arabinose, fructose, xylose porter (characterized)
to candidate WP_038022060.1 HA49_RS08470 sulfate/thiosulfate ABC transporter ATP-binding protein CysA
Query= TCDB::Q97UF2 (371 letters) >NCBI__GCF_000757425.2:WP_038022060.1 Length = 362 Score = 191 bits (485), Expect = 3e-53 Identities = 113/292 (38%), Positives = 171/292 (58%), Gaps = 14/292 (4%) Query: 3 TIRVENLSKIFKKGKTEVKAVDNVSITIDSGMAFGVLGPSGHGKTTFLRLIAGLEEPTSG 62 +I + ++K F GKT V ++++ + I SG +LGPSG GKTT LR+IAGLE SG Sbjct: 2 SINIHQINKSF--GKTPV--LNDIDLDISSGEMVALLGPSGSGKTTLLRIIAGLEHQNSG 57 Query: 63 YIYFDNEAVSSPRRVMMSPEKRGIAMVFQNWALYPNMTVFDNIAFPLKLA----KVPKDK 118 I F + VS + R + VFQ++AL+ +MTVFDNIAF L + + + Sbjct: 58 RISFRDRDVSH-----LHARDRHVGFVFQHYALFRHMTVFDNIAFGLTVLPRRERPSQAD 112 Query: 119 IENKVKEVSEELGLSGVLNRYPKELSGGQMQRTAIARALVKDPKVLLLDEPFSNLDAQIR 178 I KV + E + LS + RYP +LSGGQ QR A+ARAL DP +LLLDEPF LDAQ+R Sbjct: 113 IRKKVLNLLEMVQLSHLAGRYPAQLSGGQKQRVALARALAVDPHILLLDEPFGALDAQVR 172 Query: 179 ESARALVRKIQRERKLTTLIVSHDPADIFAIANKAGVIVNGKFAQIGTPTEIYEYPATDL 238 + R +R++ E + T++ V+HD + +A++ V+ G Q GTP ++++ PA+ Sbjct: 173 KELRRWLRQLHEELQFTSVFVTHDQEEAMEVADRIVVMSQGNVEQTGTPEQVWKQPASRF 232 Query: 239 IARLTGEINLIQAKIIENNAIIANLKVPLNNMELKGQSNIVIGLRPDDLTLS 290 + GEIN +Q +++ N +A + PL + Q + + LRP + +S Sbjct: 233 VLEFLGEINRLQGQLVGNKLQVAGHQWPL-DFTPAVQGEVDLFLRPWETDIS 283 Lambda K H 0.317 0.136 0.374 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: 260 Number of extensions: 11 Number of successful extensions: 4 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: 371 Length of database: 362 Length adjustment: 30 Effective length of query: 341 Effective length of database: 332 Effective search space: 113212 Effective search space used: 113212 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 49 (23.5 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