Align AraV, component of Arabinose, fructose, xylose porter (characterized)
to candidate GFF776 PGA1_c07900 alpha-glucoside transport ATP-binding protein AglK
Query= TCDB::Q97UF2 (371 letters) >FitnessBrowser__Phaeo:GFF776 Length = 363 Score = 194 bits (493), Expect = 3e-54 Identities = 118/334 (35%), Positives = 191/334 (57%), Gaps = 33/334 (9%) Query: 1 MTTIRVENLSKIFKKGKTEVKAVDNVSITIDSGMAFGVLGPSGHGKTTFLRLIAGLEEPT 60 M +++ N++K + G V+ + ++++ I G +GPSG GK+T LR+IAGLE + Sbjct: 1 MANLKLTNVAKTYGGG---VEVLRDINLDIKQGELIVFVGPSGCGKSTLLRMIAGLERIS 57 Query: 61 SGYIYFDNEAVSSPRRVMMSPEKRGIAMVFQNWALYPNMTVFDNIAFPLKLAKVPKDKIE 120 G + DN ++ + P +RGIAMVFQ++ALYP+MTV DN+AF LK+AK KD+I+ Sbjct: 58 GGTLEIDNAVMND-----IPPAQRGIAMVFQSYALYPHMTVRDNMAFALKIAKKSKDEID 112 Query: 121 NKVKEVSEELGLSGVLNRYPKELSGGQMQRTAIARALVKDPKVLLLDEPFSNLDAQIRES 180 + ++ L L L+R PK LSGGQ QR AI R++V+DPKV L DEP SNLDA +R + Sbjct: 113 AAIDRAAKILQLEPYLDRLPKALSGGQRQRVAIGRSIVRDPKVYLFDEPLSNLDAALRVA 172 Query: 181 ARALVRKIQRERKLTTLI-VSHDPADIFAIANKAGVIVNGKFAQIGTPTEIYEYPATDLI 239 R + +++ +T+I V+HD + +A++ V+ + AQ+GTP ++Y+ P + + Sbjct: 173 TRIEIAQLKEAMPDSTMIYVTHDQVEAMTLASRIVVLADKGIAQVGTPLDLYQRPENEFV 232 Query: 240 ARLTGE--INLIQAKII-----------ENNAIIANLKVPLNNMELKGQSNIVIGLRPDD 286 A+ G +NLI ++ ++A + + L + +G+RP+D Sbjct: 233 AQFIGSPAMNLIPGTVVATGPRTTVRLTSGEEVVAEIPTTDADQGLA----VNVGVRPED 288 Query: 287 LTLSDT---LLDKYID----MGIVKVKLVSYGAG 313 L T L+D +D +G V V ++ G G Sbjct: 289 LVEEGTGGALIDSRVDIVEALGEVTVLYIAAGEG 322 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: 303 Number of extensions: 15 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: 363 Length adjustment: 30 Effective length of query: 341 Effective length of database: 333 Effective search space: 113553 Effective search space used: 113553 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