Align AraV, component of Arabinose, fructose, xylose porter (characterized)
to candidate WP_047006727.1 AAW01_RS07155 ATP-binding cassette domain-containing protein
Query= TCDB::Q97UF2 (371 letters) >NCBI__GCF_001010925.1:WP_047006727.1 Length = 255 Score = 122 bits (306), Expect = 1e-32 Identities = 78/229 (34%), Positives = 121/229 (52%), Gaps = 12/229 (5%) Query: 4 IRVENLSKIFKKGKTEVKAVDNVSITIDSGMAFGVLGPSGHGKTTFLRLIAGLEEPTSGY 63 +R+ LSK + + AVD VS+ I +G ++G SG GK+T L+ + L EP G Sbjct: 9 LRIAGLSKTYDGAR----AVDTVSLEIGAGEFVALVGASGSGKSTLLKCVNRLVEPDEGS 64 Query: 64 IYFDNEAVSSPRRVMMSPEKRGIAMVFQNWALYPNMTVFDNIAFPLKLAK--VPKDKIEN 121 + D + + + + +R I VFQ L+P++TV NIA P +L + D+I Sbjct: 65 VQIDGQDTAG---LPPAESRRRIGYVFQGIGLFPHLTVAQNIALPSRLESNALSADRIAE 121 Query: 122 KVKEVSEELGLSGVLNRYPKELSGGQMQRTAIARALVKDPKVLLLDEPFSNLDAQIRESA 181 + V E ++ R P ELSGGQ QR +ARAL + +LL+DEPF LD R Sbjct: 122 LLALVELEPEMA---QRMPSELSGGQRQRVGVARALSSESHLLLMDEPFGALDPLTRGEL 178 Query: 182 RALVRKIQRERKLTTLIVSHDPADIFAIANKAGVIVNGKFAQIGTPTEI 230 VR++ + LTT++V+HD A+ +A + V+ +G+ TP + Sbjct: 179 GKRVRRLHDQLHLTTVLVTHDMAEALLLATRVLVMDSGRIVADETPAAL 227 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: 188 Number of extensions: 7 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: 255 Length adjustment: 27 Effective length of query: 344 Effective length of database: 228 Effective search space: 78432 Effective search space used: 78432 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 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