Align AraV, component of Arabinose, fructose, xylose porter (characterized)
to candidate Ga0059261_2293 Ga0059261_2293 cell division ATP-binding protein FtsE
Query= TCDB::Q97UF2 (371 letters) >FitnessBrowser__Korea:Ga0059261_2293 Length = 235 Score = 119 bits (297), Expect = 1e-31 Identities = 71/217 (32%), Positives = 118/217 (54%), Gaps = 3/217 (1%) Query: 18 TEVKAVDNVSITIDSGMAFGVLGPSGHGKTTFLRLIAGLEEPTSGYIYFDNEAVSSPRRV 77 T + + +VS T+ +G + V G SG GKT+ LRL+ + PT G + E + R Sbjct: 16 TGAETLSDVSFTLSAGSFYFVTGASGAGKTSLLRLLYLAQRPTRGIVRLFGEDAGALPRK 75 Query: 78 MMSPEKRGIAMVFQNWALYPNMTVFDNIAFPLKLAKVPKDKIENKVKEVSEELGLSGVLN 137 + +R I +VFQ++ L P+++ +DN+A PL++A +P+ IE V+E+ +GL + Sbjct: 76 RLPGFRRRIGVVFQDFRLLPHLSAYDNVALPLRVAGIPEADIEGPVREMIAWVGLKDRDS 135 Query: 138 RYPKELSGGQMQRTAIARALVKDPKVLLLDEPFSNLDAQIRESARALVRKIQRERKLTTL 197 P LSGG+ QR AIARA++ P++L+ DEP N+D + E L + R T + Sbjct: 136 AKPPTLSGGEQQRIAIARAVITRPEILIADEPTGNVDPDMAERLLHLFDSLNR-LGTTVV 194 Query: 198 IVSHDPADIFAIANKAGVIVNGKFAQIGTPTEIYEYP 234 + +HD I I + ++ + ++ PT YP Sbjct: 195 VATHDFQLISRIPDAR--MMRIEKGRLNDPTGALRYP 229 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: 183 Number of extensions: 7 Number of successful extensions: 1 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: 235 Length adjustment: 26 Effective length of query: 345 Effective length of database: 209 Effective search space: 72105 Effective search space used: 72105 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: 48 (23.1 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