Align AraV, component of Arabinose, fructose, xylose porter (characterized)
to candidate WP_008538413.1 HMPREF9454_RS05390 ABC transporter ATP-binding protein
Query= TCDB::Q97UF2 (371 letters) >NCBI__GCF_000245775.1:WP_008538413.1 Length = 260 Score = 186 bits (473), Expect = 5e-52 Identities = 103/249 (41%), Positives = 153/249 (61%), Gaps = 11/249 (4%) Query: 11 KIFKKGKTEVKAVDNVSITIDSGMAFGVLGPSGHGKTTFLRLIAGLEEPTSGYIYFDNEA 70 K +K ++ + N+++ I+ G +LGPSG GKTT L LI GL + + G I FD E Sbjct: 5 KKIRKSYEGIEVLKNINLKIEKGEIVSILGPSGCGKTTLLNLILGLTQVSEGRIIFDGED 64 Query: 71 VSSPRRVMMSPEKRGIAMVFQNWALYPNMTVFDNIAFPLKLAKVPKDKIENKVKEVSEEL 130 ++ M EKRG +VFQ++AL+PN+ V++NI + LK P +V+++ L Sbjct: 65 ITQ-----MPMEKRGFNIVFQDYALFPNLNVYENIVYGLK--NKPNISTTKEVQDLINLL 117 Query: 131 GLSGVLNRYPKELSGGQMQRTAIARALVKDPKVLLLDEPFSNLDAQIRESARALVRKIQR 190 GL L + +ELSGGQ QRTA+AR LV PK+LLLDEP S LD I+ES + +++I R Sbjct: 118 GLGKHLTKKIEELSGGQKQRTALARTLVMKPKILLLDEPLSALDGVIKESIKQKIKEIAR 177 Query: 191 ERKLTTLIVSHDPADIFAIANKAGVIVNGKFAQIGTPTEIYEYPATDLIARLTGEINLIQ 250 + KLTT+IV+HDP + +++K ++ G+ +Q GTP EI + PA D ++ E L Q Sbjct: 178 DFKLTTIIVTHDPEEALTLSDKVLIVNEGQISQFGTPEEIIKKPANDFVS----EFILRQ 233 Query: 251 AKIIENNAI 259 +I NN + Sbjct: 234 LEIKRNNIL 242 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: 242 Number of extensions: 15 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: 260 Length adjustment: 27 Effective length of query: 344 Effective length of database: 233 Effective search space: 80152 Effective search space used: 80152 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