Align AraV, component of Arabinose, fructose, xylose porter (characterized)
to candidate WP_025329853.1 SALWKB2_RS01070 sulfate ABC transporter ATP-binding protein
Query= TCDB::Q97UF2 (371 letters) >NCBI__GCF_000600005.1:WP_025329853.1 Length = 360 Score = 183 bits (464), Expect = 7e-51 Identities = 107/317 (33%), Positives = 186/317 (58%), Gaps = 16/317 (5%) Query: 3 TIRVENLSKIFKKGKTEVKAVDNVSITIDSGMAFGVLGPSGHGKTTFLRLIAGLEEPTSG 62 +IR++ L+K + + +A+ N+++ + +G +LGPSG GKTT LR+IAGLE SG Sbjct: 2 SIRIKQLNKYYG----DYQALQNINLQVPTGSLTALLGPSGCGKTTLLRIIAGLERADSG 57 Query: 63 YIYFDNEAVSSPRRVMMSPEKRGIAMVFQNWALYPNMTVFDNIAFPL----KLAKVPKDK 118 ++F ++ VS+ + +R + +FQ++AL+ +MTVFDN+AF L K + K + Sbjct: 58 ELFFADDEVSN-----LHVRERRVGFMFQHYALFRHMTVFDNVAFGLQVLPKRIRPNKAE 112 Query: 119 IENKVKEVSEELGLSGVLNRYPKELSGGQMQRTAIARALVKDPKVLLLDEPFSNLDAQIR 178 I ++V E+ + + L + YP++LSGGQ QR A+ARAL PK+LLLDEPF LDA++R Sbjct: 113 IADRVHELLQLVQLDWLAKVYPQQLSGGQRQRIALARALATRPKLLLLDEPFGALDAKVR 172 Query: 179 ESARALVRKIQRERKLTTLIVSHDPADIFAIANKAGVIVNGKFAQIGTPTEIYEYPATDL 238 + R + +I + +T+++V+HD + +A + V+ GK Q G + +Y+ P Sbjct: 173 KELRQWLLEIHHQLGITSVLVTHDQEEALEMAEQIVVMNQGKVEQSGAASSLYDNPENVF 232 Query: 239 IARLTGEINLIQAKIIENNAI-IANLKVPLNNMELKGQSNIVIGLRPDDLTLSDTLLDKY 297 + GE+N+ + IE+ + + + P+ E K + N+ + +RP ++ + + D Sbjct: 233 VTEFLGEVNVFEDACIEHGQLCLGHYHEPITTGE-KARQNVAVYIRPQEVQVLTHIQDNI 291 Query: 298 IDMGIVKVKLVSYGAGI 314 I V+ K+ + GA I Sbjct: 292 IASACVE-KIHAIGAQI 307 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: 270 Number of extensions: 11 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: 360 Length adjustment: 30 Effective length of query: 341 Effective length of database: 330 Effective search space: 112530 Effective search space used: 112530 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 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