Align Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale)
to candidate WP_069331237.1 C8J29_RS14155 sn-glycerol-3-phosphate import ATP-binding protein UgpC
Query= uniprot:D4GP39 (383 letters) >NCBI__GCF_003046325.1:WP_069331237.1 Length = 349 Score = 298 bits (762), Expect = 2e-85 Identities = 174/369 (47%), Positives = 228/369 (61%), Gaps = 23/369 (6%) Query: 1 MARLTLDDVTKVYTDEGGGDIVAVEEISLDIDDGEFLVLVGPSGCGKSTTLRMMAGLETV 60 MA ++L DV K Y+ + + + L+I DGEF+V+VGPSGCGKST LRM+AGLE + Sbjct: 1 MAEISLRDVRKSYSG-----LEVIHGVDLEIADGEFVVIVGPSGCGKSTLLRMVAGLEEI 55 Query: 61 TEGELRLEDRVLNGVSAQDRDIAMVFQSYALYPHKSVRGNMSFGLEESTGLPDDEIRQRV 120 T GE+ + RV+N + ++RDIAMVFQ+YALYPH +VR NM++GL + L EI +RV Sbjct: 56 TAGEIAIGGRVVNRLEPRERDIAMVFQNYALYPHMTVRENMAYGLRIAK-LSKAEIEERV 114 Query: 121 EETTDMLGISDLLDRKPGQLSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRT 180 + ML + LLDRKP QLSGGQ+QRVA+GRA+VR+P FL+DEPLSNLDAKLR +MR Sbjct: 115 ARSAKMLELGQLLDRKPRQLSGGQRQRVAMGRALVRNPAAFLLDEPLSNLDAKLRVQMRL 174 Query: 181 ELQRLQGELGVTTVYVTHDQTEAMTMGDRVAVLDDGELQQVGTPLDCYHRPNNLFVAGFI 240 +++ LQ + T++YVTHDQ EAMT+ DR+ V++ G +Q+ TP + Y RP FVAGFI Sbjct: 175 QIKELQRTVRTTSIYVTHDQVEAMTLADRLVVMNAGVAEQIATPAEIYDRPATTFVAGFI 234 Query: 241 GEPSMNLFDGSLSGDTFR--GDGFDYPLSGATRDQLGGASGLTLGIRPEDV-TVGERRSG 297 G P+MN+ GD G P + A RD L LGIRPE + G G Sbjct: 235 GSPAMNMLPARGLGDALEVAGQRLAVP-APAGRD-------LILGIRPEHLHPAGPEEPG 286 Query: 298 QRTFDAEVVVVEPQGNENAVHLRFVDGDEGTQFTATTTGQSRVEAGDRTTVSFPEDAIHL 357 F+ V VE G + H D GT T G++ V DR V+ A+HL Sbjct: 287 ---FELHVQAVEWLGADAFAHGSLAD---GTDLVLRTPGKAPVRERDRLKVAPDAAALHL 340 Query: 358 FDGETGDAL 366 FD TG L Sbjct: 341 FDAGTGRRL 349 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: 410 Number of extensions: 24 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: 383 Length of database: 349 Length adjustment: 30 Effective length of query: 353 Effective length of database: 319 Effective search space: 112607 Effective search space used: 112607 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