Align AraV, component of Arabinose, fructose, xylose porter (characterized)
to candidate WP_200806763.1 B5D49_RS03200 ABC transporter ATP-binding protein
Query= TCDB::Q97UF2 (371 letters) >NCBI__GCF_900167125.1:WP_200806763.1 Length = 406 Score = 204 bits (520), Expect = 3e-57 Identities = 111/253 (43%), Positives = 160/253 (63%), Gaps = 11/253 (4%) Query: 4 IRVENLSKIFKKGKTEVKAVDNVSITIDSGMAFGVLGPSGHGKTTFLRLIAGLEEPTSGY 63 +R++ L K F GKT AV +TI++G +LGPSG GKTT LR+IAGLE PT G Sbjct: 45 VRLQGLMKRF--GKTV--AVQETDLTIETGELVTLLGPSGCGKTTILRMIAGLETPTKGD 100 Query: 64 IYFDNEAVSSPRRVMMSP-EKRGIAMVFQNWALYPNMTVFDNIAFPLKLAKVPKDKIENK 122 IY RR+ +P KR + M+FQN+AL+P+ T+F+N+AF LK V ++++ K Sbjct: 101 IYIKG------RRINDTPIHKRNLGMIFQNYALFPHKTIFENVAFGLKYRNVSREEMREK 154 Query: 123 VKEVSEELGLSGVLNRYPKELSGGQMQRTAIARALVKDPKVLLLDEPFSNLDAQIRESAR 182 V + E + L GV RY +LSGGQ QR A+ARA+V +P VLL+DEP S LD ++RE R Sbjct: 155 VAQALEMVRLPGVEKRYASQLSGGQQQRIALARAIVIEPDVLLMDEPLSALDEKLREEMR 214 Query: 183 ALVRKIQRERKLTTLIVSHDPADIFAIANKAGVIVNGKFAQIGTPTEIYEYPATDLIARL 242 + IQ++ LTTL V+HD + +++NK V+ +G+ Q GTP ++Y+YP +A Sbjct: 215 MEIDNIQQQLNLTTLFVTHDQREALSMSNKIVVMKDGRKQQEGTPEDVYDYPDNYFVADF 274 Query: 243 TGEINLIQAKIIE 255 G N A+++E Sbjct: 275 LGHANFFDARVLE 287 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: 319 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: 406 Length adjustment: 30 Effective length of query: 341 Effective length of database: 376 Effective search space: 128216 Effective search space used: 128216 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 Apr 09 2024. 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