Align AraV, component of Arabinose, fructose, xylose porter (characterized)
to candidate 14400 b0262 putative ATP-binding component of a transport system (VIMSS)
Query= TCDB::Q97UF2 (371 letters) >FitnessBrowser__Keio:14400 Length = 348 Score = 212 bits (540), Expect = 1e-59 Identities = 114/288 (39%), Positives = 181/288 (62%), Gaps = 10/288 (3%) Query: 4 IRVENLSKIFKKGKTEVKAVDNVSITIDSGMAFGVLGPSGHGKTTFLRLIAGLEEPTSGY 63 + + N++K F G V +DN+++TI G +LGPSG GKTT LRL+AGLE+P+ G Sbjct: 7 VELRNVTKRF--GSNTV--IDNINLTIPQGQMVTLLGPSGCGKTTILRLVAGLEKPSEGQ 62 Query: 64 IYFDNEAVSSPRRVMMSPEKRGIAMVFQNWALYPNMTVFDNIAFPLKLAKVPKDKIENKV 123 I+ D E V+ S ++R I MVFQ++AL+P+M++ +N+ + LK+ VP+ +++ +V Sbjct: 63 IFIDGEDVTH-----RSIQQRDICMVFQSYALFPHMSLGENVGYGLKMLGVPRAELKARV 117 Query: 124 KEVSEELGLSGVLNRYPKELSGGQMQRTAIARALVKDPKVLLLDEPFSNLDAQIRESARA 183 KE + L G +R+ ++SGGQ QR A+ARAL+ PKVLL DEP SNLDA +R S R Sbjct: 118 KEALAMVDLEGFEDRFVDQISGGQQQRVALARALILKPKVLLFDEPLSNLDANLRRSMRD 177 Query: 184 LVRKIQRERKLTTLIVSHDPADIFAIANKAGVIVNGKFAQIGTPTEIYEYPATDLIARLT 243 +R++Q++ +T+L V+HD ++ FA+++ V+ G QIG+P ++Y PA+ +A Sbjct: 178 KIRELQKQFDITSLYVTHDQSEAFAVSDTVLVMNKGHIMQIGSPQDLYRQPASRFMASFM 237 Query: 244 GEINLIQAKIIENNAIIANLKVPLNNMELKGQSNIVIGLRPDDLTLSD 291 G+ NL A + I +P + Q ++G+RP+ +TLSD Sbjct: 238 GDANLFPATFSDGYVDIYGYHLP-RPLHFGTQGEGMVGVRPEAITLSD 284 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: 264 Number of extensions: 11 Number of successful extensions: 2 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: 348 Length adjustment: 29 Effective length of query: 342 Effective length of database: 319 Effective search space: 109098 Effective search space used: 109098 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