Align AraV, component of Arabinose, fructose, xylose porter (characterized)
to candidate WP_010538975.1 KCY_RS0121335 glycine betaine/L-proline ABC transporter ATP-binding protein
Query= TCDB::Q97UF2 (371 letters) >NCBI__GCF_000226135.1:WP_010538975.1 Length = 408 Score = 154 bits (389), Expect = 4e-42 Identities = 99/305 (32%), Positives = 170/305 (55%), Gaps = 13/305 (4%) Query: 11 KIFKKGKTEVK---------AVDNVSITIDSGMAFGVLGPSGHGKTTFLRLIAGLEEPTS 61 K+ K+GKT+ + AV + +++I+ G F ++G SG GK+T LR I L PTS Sbjct: 22 KMLKEGKTKSEILKATGCTVAVKDANLSINEGEIFVIMGLSGSGKSTLLRCINRLIRPTS 81 Query: 62 GYIYFDNEAVSSPR-RVMMSPEKRGIAMVFQNWALYPNMTVFDNIAFPLKLAKVPKDKIE 120 G + + ++ + ++ ++ +AMVFQN+ L P+ +V NIAF L+L V K + E Sbjct: 82 GEVIINGTDIAKVSDKELLQIRRKELAMVFQNFGLLPHRSVLHNIAFGLELQGVKKGERE 141 Query: 121 NKVKEVSEELGLSGVLNRYPKELSGGQMQRTAIARALVKDPKVLLLDEPFSNLDAQIRES 180 K E + +GL G N+ ELSGG QR +ARAL +P+VLL+DE FS LD IR Sbjct: 142 KKAMESMQLVGLKGYENQMVSELSGGMQQRVGLARALANNPEVLLMDEAFSALDPLIRVQ 201 Query: 181 ARALVRKIQRERKLTTLIVSHDPADIFAIANKAGVIVNGKFAQIGTPTEIYEYPATDLIA 240 + + +Q + K T + ++HD ++ + ++ ++ +G+ QIGT EI PA + Sbjct: 202 MQDELLTLQSKMKKTIVFITHDLSEAIKLGDRIAIMKDGEIVQIGTSEEILTEPADAYVE 261 Query: 241 RLTGEINLIQAKIIENNAIIANLKVPLNNMELKGQSNIVIGLRPDDLTLSDTLLDKYIDM 300 R N+ ++KII ++I+ + K + ++ +G ++ +R +LT+ + I + Sbjct: 262 RFVE--NVDRSKIITASSIMVD-KPIVARLKKEGPEVLIRKMRERNLTVLPVVDSNDILV 318 Query: 301 GIVKV 305 G V++ Sbjct: 319 GEVRL 323 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: 298 Number of extensions: 10 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: 408 Length adjustment: 30 Effective length of query: 341 Effective length of database: 378 Effective search space: 128898 Effective search space used: 128898 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 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