Align AraV, component of Arabinose, fructose, xylose porter (characterized)
to candidate WP_008538734.1 HMPREF9454_RS06810 amino acid ABC transporter ATP-binding protein
Query= TCDB::Q97UF2 (371 letters) >NCBI__GCF_000245775.1:WP_008538734.1 Length = 239 Score = 142 bits (358), Expect = 9e-39 Identities = 82/232 (35%), Positives = 132/232 (56%), Gaps = 8/232 (3%) Query: 4 IRVENLSKIFKKGKTEVKAVDNVSITIDSGMAFGVLGPSGHGKTTFLRLIAGLEEPTSGY 63 I ++NL K F V+ + V ++I+ ++GPSG GK+T LR + LEEPTSG Sbjct: 2 IEIKNLHKSFG----HVEVLKGVDVSIEEKEVVVIIGPSGSGKSTLLRCMNYLEEPTSGD 57 Query: 64 IYFDNEAVSSPRRVMMSPEKRGIAMVFQNWALYPNMTVFDNIAF-PLKLAKVPKDKIENK 122 I DN + + ++ + I MVFQ + L+P+MTV +NI P K+ K+ +D+ + Sbjct: 58 ITVDNMKLD--KHADINKIRENIGMVFQRFNLFPHMTVLENIVLAPTKVLKISRDEAIST 115 Query: 123 VKEVSEELGLSGVLNRYPKELSGGQMQRTAIARALVKDPKVLLLDEPFSNLDAQIRESAR 182 ++ + +GL N YP +LSGGQ QR AIARAL PKV+L DEP S LD ++ Sbjct: 116 AMDLLQRVGLKEKANSYPSQLSGGQQQRVAIARALAMKPKVMLFDEPTSALDPEMVTEVL 175 Query: 183 ALVRKIQRERKLTTLIVSHDPADIFAIANKAGVIVNGKFAQIGTPTEIYEYP 234 +++ + + +T ++V+H+ + ++ + G+ + GTP EI+E P Sbjct: 176 DVMKSLANQ-GMTMVVVTHEMGFAREVGDRVLFVDEGRIIEEGTPKEIFENP 226 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: 243 Number of extensions: 14 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: 239 Length adjustment: 26 Effective length of query: 345 Effective length of database: 213 Effective search space: 73485 Effective search space used: 73485 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 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