Align AraV, component of Arabinose, fructose, xylose porter (characterized)
to candidate WP_092482139.1 BM299_RS03860 glycine betaine/L-proline ABC transporter ATP-binding protein
Query= TCDB::Q97UF2 (371 letters) >NCBI__GCF_900115975.1:WP_092482139.1 Length = 390 Score = 158 bits (400), Expect = 2e-43 Identities = 95/299 (31%), Positives = 163/299 (54%), Gaps = 25/299 (8%) Query: 4 IRVENLSKIF-----------KKGKTEVKAVD---------NVSITIDSGMAFGVLGPSG 43 + V+NL+KIF K+G ++ K ++ N S ++ G F ++G SG Sbjct: 5 VEVKNLTKIFGRNPKAILEKVKQGMSKEKILEDTGHTVGIRNASFQVEEGEVFVIMGLSG 64 Query: 44 HGKTTFLRLIAGLEEPTSGYIYFDNEAVSS-PRRVMMSPEKRGIAMVFQNWALYPNMTVF 102 GK+T +R + L +PT+G IY D + + ++ + + +AMVFQ++ L + TV Sbjct: 65 SGKSTLIRCLNLLNKPTAGEIYVDGDNILEYDKKQLKKFRQEKVAMVFQHFGLLSHRTVI 124 Query: 103 DNIAFPLKLAKVPKDKIENKVKEVSEELGLSGVLNRYPKELSGGQMQRTAIARALVKDPK 162 N+ + L++ K+PK++ K+ GL+G N+ P ELSGG QR +ARAL DP Sbjct: 125 GNVEYGLEVKKIPKNERCEIAKKAIANAGLAGWENKMPNELSGGMQQRVGLARALANDPD 184 Query: 163 VLLLDEPFSNLDAQIRESARALVRKIQRERKLTTLIVSHDPADIFAIANKAGVIVNGKFA 222 +LL+DEPFS LD IR + + ++Q K T + ++HD + F I ++ V+ +G Sbjct: 185 ILLMDEPFSALDPLIRRDMQYELMELQSRLKKTIIFITHDINEAFKIGDRVAVMKDGVIE 244 Query: 223 QIGTPTEIYEYPATDLIARLTGEIN---LIQAK-IIENNAIIANLKVPLNNMELKGQSN 277 QIGTP E+ P ++ I +I+ ++QAK ++ ++ ++K L ++ +SN Sbjct: 245 QIGTPEELLASPESEYIENFVKDIDRSKVLQAKHVMFKPTVLVSIKEGLKAAMMEMKSN 303 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: 321 Number of extensions: 15 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: 390 Length adjustment: 30 Effective length of query: 341 Effective length of database: 360 Effective search space: 122760 Effective search space used: 122760 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