Align AraV, component of Arabinose, fructose, xylose porter (characterized)
to candidate GFF1860 Psest_1899 ABC-type sugar transport systems, ATPase components
Query= TCDB::Q97UF2 (371 letters) >FitnessBrowser__psRCH2:GFF1860 Length = 390 Score = 198 bits (504), Expect = 2e-55 Identities = 111/302 (36%), Positives = 174/302 (57%), Gaps = 19/302 (6%) Query: 1 MTTIRVENLSKIFKKGKTEVKAVDNVSITIDSGMAFGVLGPSGHGKTTFLRLIAGLEEPT 60 M ++ + N+ K + G +++ + ++++ ID+G ++GPSG GK+T + IAGLE T Sbjct: 1 MASLELRNVQKSY--GNSQIATLKDIALKIDAGEFLILVGPSGCGKSTLMNCIAGLENIT 58 Query: 61 SGYIYFDNEAVSSPRRVMMSPEKRGIAMVFQNWALYPNMTVFDNIAFPLKLAKVPKDKIE 120 G I D E +S SP+ R IAMVFQ++ALYP M+V DNIAF LK+ KVP KIE Sbjct: 59 GGEILVDGEDISQA-----SPKDRDIAMVFQSYALYPTMSVRDNIAFGLKMRKVPAAKIE 113 Query: 121 NKVKEVSEELGLSGVLNRYPKELSGGQMQRTAIARALVKDPKVLLLDEPFSNLDAQIRES 180 +V V++ L + +L R P +LSGGQ QR A+ RAL + PK+ L DEP SNLDA++R Sbjct: 114 EEVARVAKLLQIEPLLERKPSQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVE 173 Query: 181 ARALVRKIQRERKLTTLIVSHDPADIFAIANKAGVIVNGKFAQIGTPTEIYEYPATDLIA 240 R ++ + + K TT+ V+HD + + +K V+ +G Q GTP EIY PA +A Sbjct: 174 MRTEIKLMHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGVIQQFGTPHEIYNNPANLFVA 233 Query: 241 RLTGE--INLIQAKI----------IENNAIIANLKVPLNNMELKGQSNIVIGLRPDDLT 288 G +N + +I + + L +P+ + + +++G+RP+ + Sbjct: 234 SFIGSPPMNFVPLRIRQRDGRWVGVLNSEQGSCELPLPITSDDGLRDRELILGIRPEQIG 293 Query: 289 LS 290 L+ Sbjct: 294 LA 295 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: 307 Number of extensions: 17 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: 390 Length adjustment: 30 Effective length of query: 341 Effective length of database: 360 Effective search space: 122760 Effective search space used: 122760 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: 50 (23.9 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