Align AraV, component of Arabinose, fructose, xylose porter (characterized)
to candidate Ac3H11_4785 Glycerol-3-phosphate ABC transporter, ATP-binding protein UgpC (TC 3.A.1.1.3)
Query= TCDB::Q97UF2 (371 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_4785 Length = 334 Score = 201 bits (511), Expect = 2e-56 Identities = 104/252 (41%), Positives = 160/252 (63%), Gaps = 7/252 (2%) Query: 1 MTTIRVENLSKIFKKGKTEVKAVDNVSITIDSGMAFGVLGPSGHGKTTFLRLIAGLEEPT 60 M ++ + N++K + G + + V+ + G ++GPSG GK+T LR++AGLEE + Sbjct: 1 MASLSLRNITKRYGHGPKANQVIHGVNAEVKDGEFVVIVGPSGCGKSTLLRMVAGLEEIS 60 Query: 61 SGYIYFDNEAVSSPRRVMMSPEKRGIAMVFQNWALYPNMTVFDNIAFPLKLAKVPKDKIE 120 G + + V+ + P +R IAMVFQN+ALYP+MT F+N+A+ LK+AKVPKD+I+ Sbjct: 61 GGELRIGDRVVND-----LEPAQRDIAMVFQNYALYPHMTNFENMAYGLKIAKVPKDEIK 115 Query: 121 NKVKEVSEELGLSGVLNRYPKELSGGQMQRTAIARALVKDPKVLLLDEPFSNLDAQIRES 180 +V + ++ L L +L R P+ELSGGQ QR A+ RA+V+ P+V L DEP SNLDA++R Sbjct: 116 ARVDKAAKILELGHLLERKPRELSGGQRQRVAMGRAIVRQPQVFLFDEPLSNLDAKLRAQ 175 Query: 181 ARALVRKIQRERKLTTLIVSHDPADIFAIANKAGVIVNGKFAQIGTPTEIYEYPATDLIA 240 R ++K+ RE +T+L V+HD + +A + V+ G Q GTP E+Y PAT +A Sbjct: 176 TRLEIQKLHRELGITSLFVTHDQVEAMTLAQRMIVMNAGNMEQFGTPEEVYHTPATTFVA 235 Query: 241 RLTGE--INLIQ 250 G +NL++ Sbjct: 236 SFIGSPPMNLLK 247 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: 280 Number of extensions: 12 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: 334 Length adjustment: 29 Effective length of query: 342 Effective length of database: 305 Effective search space: 104310 Effective search space used: 104310 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