Align AraV, component of Arabinose, fructose, xylose porter (characterized)
to candidate H281DRAFT_02040 H281DRAFT_02040 putative spermidine/putrescine transport system ATP-binding protein
Query= TCDB::Q97UF2 (371 letters) >FitnessBrowser__Burk376:H281DRAFT_02040 Length = 356 Score = 199 bits (505), Expect = 1e-55 Identities = 119/298 (39%), Positives = 176/298 (59%), Gaps = 22/298 (7%) Query: 1 MTTIRVENLSKIFKKGKTEVKAVDNVSITIDSGMAFGVLGPSGHGKTTFLRLIAGLEEPT 60 M + +ENL K F T + A+ + + I+ G LGPSG GKTT LR+IAG E PT Sbjct: 1 MAFLEIENLHKSFG---TNI-ALHHFDMKIERGEFITFLGPSGCGKTTVLRMIAGFETPT 56 Query: 61 SGYIYFDNEAVSSPRRVMMSPEKRGIAMVFQNWALYPNMTVFDNIAFPLKLAKVPKDKIE 120 G I DN+ V+ R +R + MVFQ++AL+PNMTV +NI F LK+ P+ +I Sbjct: 57 RGVIRLDNKDVTHLRT-----RQRKVGMVFQSYALFPNMTVAENIGFGLKITHRPQAEIS 111 Query: 121 NKVKEVSEELGLSGVLNRYPKELSGGQMQRTAIARALVKDPKVLLLDEPFSNLDAQIRES 180 +V+E+ + L + RYP +LSGGQ QR A+ARAL P+VLLLDEP S LDA+IR S Sbjct: 112 QRVEEMLHLIKLPQLGGRYPWQLSGGQQQRVALARALAGKPQVLLLDEPLSALDAKIRIS 171 Query: 181 ARALVRKIQRERKLTTLIVSHDPADIFAIANKAGVIVNGKFAQIGTPTEIYEYPATDLIA 240 R +R +QRE +T++ V+HD + +I+++ V+ G+ QIG+P+EIY YP T +A Sbjct: 172 LRQDIRALQRELGITSIFVTHDQEEALSISDRIVVMNEGRVEQIGSPSEIYNYPRTRFVA 231 Query: 241 RLTGEINLIQAKIIENNAIIANLKVPLNNMELKGQSNI---------VIGLRPDDLTL 289 G +N++ +I+ A K+ ++ EL + ++ LRP+ + L Sbjct: 232 SFVGTLNILAGHVIDP----ATGKMVVDGQELTTTQELPAGDAGKKRLLALRPEAIVL 285 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: 302 Number of extensions: 5 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: 356 Length adjustment: 29 Effective length of query: 342 Effective length of database: 327 Effective search space: 111834 Effective search space used: 111834 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