Align AraV, component of Arabinose, fructose, xylose porter (characterized)
to candidate Echvi_3653 Echvi_3653 ABC-type sulfate/molybdate transport systems, ATPase component
Query= TCDB::Q97UF2 (371 letters) >FitnessBrowser__Cola:Echvi_3653 Length = 290 Score = 148 bits (373), Expect = 2e-40 Identities = 94/237 (39%), Positives = 137/237 (57%), Gaps = 11/237 (4%) Query: 14 KKGKTEVKAVD-NVSITIDSGMAFGVLGPSGHGKTTFLRLIAGLEEPTSGYIYFDNEA-- 70 K K A+D ++ +TI G + GPSG GKT+ LR+I+GL P G++ + E Sbjct: 8 KSLKANGPAMDLDIKLTISQGEFITLFGPSGSGKTSTLRMISGLLTPDKGHLSVNGEQWF 67 Query: 71 -VSSPRRVMMSPEKRGIAMVFQNWALYPNMTVFDNIAFPLKLAKVPKDKIENKVKEVSEE 129 S + V SP +R + +FQ+++L+PNMTV +NIAF LK AK DK + E+ E Sbjct: 68 DASFGKNV--SPGRRKLGYLFQDYSLFPNMTVKENIAFALKNAK---DKAY--LMELLES 120 Query: 130 LGLSGVLNRYPKELSGGQMQRTAIARALVKDPKVLLLDEPFSNLDAQIRESARALVRKIQ 189 +GL + + PK LSGGQ QR A+ARAL P +LLLDEP S LD +RE + + I Sbjct: 121 MGLLHLQDTLPKHLSGGQQQRVALARALALKPDILLLDEPLSALDPSMREKLQEYILAIH 180 Query: 190 RERKLTTLIVSHDPADIFAIANKAGVIVNGKFAQIGTPTEIYEYPATDLIARLTGEI 246 R+ LTT++VSHD +I ++++ + +GK + TP E + T + GEI Sbjct: 181 RKYALTTILVSHDAGEIIKLSDRIIELDHGKVLRQCTPKEFFGTGLTSAKFQFQGEI 237 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: 235 Number of extensions: 8 Number of successful extensions: 3 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: 290 Length adjustment: 28 Effective length of query: 343 Effective length of database: 262 Effective search space: 89866 Effective search space used: 89866 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 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