Align AraV, component of Arabinose, fructose, xylose porter (characterized)
to candidate WP_012048833.1 SWIT_RS13320 amino acid ABC transporter ATP-binding protein
Query= TCDB::Q97UF2 (371 letters) >NCBI__GCF_000016765.1:WP_012048833.1 Length = 241 Score = 132 bits (332), Expect = 1e-35 Identities = 74/214 (34%), Positives = 124/214 (57%), Gaps = 3/214 (1%) Query: 22 AVDNVSITIDSGMAFGVLGPSGHGKTTFLRLIAGLEEPTSGYIYFDNEAVSSPRRVMMSP 81 A+ NVS+ + G + GPSG GK+T +R I GLE G I + V RRV+ Sbjct: 16 ALRNVSLDVARGERIVICGPSGSGKSTLIRCINGLETHDEGVIRIGEDEVRPDRRVLQRI 75 Query: 82 EKRGIAMVFQNWALYPNMTVFDNIAF-PLKLAKVPKDKIENKVKEVSEELGLSGVLNRYP 140 R + MVFQ++ L+P++T+ +N A P+K+ + +D E +E+ E + ++ ++YP Sbjct: 76 RAR-VGMVFQDFNLFPHLTILENCALAPMKVRGLARDAAEALARELLERVRIADQADKYP 134 Query: 141 KELSGGQMQRTAIARALVKDPKVLLLDEPFSNLDAQIRESARALVRKIQRERKLTTLIVS 200 +LSGGQ QRTAIARAL P+++L DEP S LDA++ + +++ + E +T L V+ Sbjct: 135 AQLSGGQQQRTAIARALAMQPEIILFDEPTSALDAEMVKEVLDIMKALATE-GITMLCVT 193 Query: 201 HDPADIFAIANKAGVIVNGKFAQIGTPTEIYEYP 234 H+ +A++ + G+ + G+P + + P Sbjct: 194 HEMGFAREVADRIIFMDAGQIVETGSPRDFFTAP 227 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: 186 Number of extensions: 12 Number of successful extensions: 4 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: 241 Length adjustment: 27 Effective length of query: 344 Effective length of database: 214 Effective search space: 73616 Effective search space used: 73616 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: 48 (23.1 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