Align Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale)
to candidate WP_110804036.1 C8J30_RS01990 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC
Query= uniprot:D4GP39 (383 letters) >NCBI__GCF_003217355.1:WP_110804036.1 Length = 361 Score = 242 bits (617), Expect = 1e-68 Identities = 144/304 (47%), Positives = 184/304 (60%), Gaps = 27/304 (8%) Query: 1 MARLTLDDVTKVYTDEGGGDIVAVEEISLDIDDGEFLVLVGPSGCGKSTTLRMMAGLETV 60 MA L L V K Y G++ + +I+LDI GE +V VGPSGCGKST LRM+AGLE + Sbjct: 1 MADLKLTRVGKSY-----GEVDVLRDINLDIKAGELIVFVGPSGCGKSTLLRMIAGLERI 55 Query: 61 TEGELRLEDRVLNGVSAQDRDIAMVFQSYALYPHKSVRGNMSFGLEESTGLPDDEIRQRV 120 + GELR++ +N + R IAMVFQSYALYPH +VR NM F L+ + D I + V Sbjct: 56 SAGELRIDGVRVNDMPPAQRGIAMVFQSYALYPHMTVRQNMEFALKIAKKTRQD-IDKAV 114 Query: 121 EETTDMLGISDLLDRKPGQLSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRT 180 E +L ++ LDR P LSGGQ+QRVA+GRAIVRDP+V+L DEPLSNLDA LR R Sbjct: 115 ENAARILQLTPYLDRLPKALSGGQRQRVAIGRAIVRDPKVYLFDEPLSNLDAALRVATRI 174 Query: 181 ELQRLQGELGV-TTVYVTHDQTEAMTMGDRVAVLDDGELQQVGTPLDCYHRPNNLFVAGF 239 E+ +L+ + T +YVTHDQ EAMT+ R+ VL + + QVGTPL+ Y +P FVA F Sbjct: 175 EIAQLKEAMPERTMIYVTHDQVEAMTLASRIVVLANKGIAQVGTPLELYEKPETEFVAQF 234 Query: 240 IGEPSMNLFDGSL------------SGDTFRGDGFDYPLSGATRDQLGGASGLTLGIRPE 287 IG P MNL G + G T R P R + +G+RPE Sbjct: 235 IGSPQMNLLPGVIRETGAVTVVALDDGGTARSTVPTSPADLGLR--------VNIGVRPE 286 Query: 288 DVTV 291 D+TV Sbjct: 287 DLTV 290 Lambda K H 0.316 0.136 0.384 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: 378 Number of extensions: 19 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: 383 Length of database: 361 Length adjustment: 30 Effective length of query: 353 Effective length of database: 331 Effective search space: 116843 Effective search space used: 116843 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: 42 (22.0 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