Align Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale)
to candidate Ac3H11_4785 Glycerol-3-phosphate ABC transporter, ATP-binding protein UgpC (TC 3.A.1.1.3)
Query= uniprot:D4GP39 (383 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_4785 Length = 334 Score = 281 bits (720), Expect = 1e-80 Identities = 164/363 (45%), Positives = 222/363 (61%), Gaps = 32/363 (8%) Query: 1 MARLTLDDVTKVYTDEGGGDIVAVEEISLDIDDGEFLVLVGPSGCGKSTTLRMMAGLETV 60 MA L+L ++TK Y G + ++ ++ DGEF+V+VGPSGCGKST LRM+AGLE + Sbjct: 1 MASLSLRNITKRY-GHGPKANQVIHGVNAEVKDGEFVVIVGPSGCGKSTLLRMVAGLEEI 59 Query: 61 TEGELRLEDRVLNGVSAQDRDIAMVFQSYALYPHKSVRGNMSFGLEESTGLPDDEIRQRV 120 + GELR+ DRV+N + RDIAMVFQ+YALYPH + NM++GL+ + +P DEI+ RV Sbjct: 60 SGGELRIGDRVVNDLEPAQRDIAMVFQNYALYPHMTNFENMAYGLKIAK-VPKDEIKARV 118 Query: 121 EETTDMLGISDLLDRKPGQLSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRT 180 ++ +L + LL+RKP +LSGGQ+QRVA+GRAIVR P+VFL DEPLSNLDAKLRA+ R Sbjct: 119 DKAAKILELGHLLERKPRELSGGQRQRVAMGRAIVRQPQVFLFDEPLSNLDAKLRAQTRL 178 Query: 181 ELQRLQGELGVTTVYVTHDQTEAMTMGDRVAVLDDGELQQVGTPLDCYHRPNNLFVAGFI 240 E+Q+L ELG+T+++VTHDQ EAMT+ R+ V++ G ++Q GTP + YH P FVA FI Sbjct: 179 EIQKLHRELGITSLFVTHDQVEAMTLAQRMIVMNAGNMEQFGTPEEVYHTPATTFVASFI 238 Query: 241 GEPSMNLFDGSLSGDTFRGDGFDYPLSGATRDQLGGASGLTLGIRPEDVTVGERRSGQRT 300 G P MNL ++ G G LGIRPE + V R G Sbjct: 239 GSPPMNLL----------------------KNAPGAQPGTILGIRPEHLDV--RSEG--- 271 Query: 301 FDAEVVVVEPQGNENAVHLRFVDGDEGTQFTATTTGQSRVEAGDRTTVSFPEDAIHLFDG 360 + V VE G E ++ R ++G++ G E V D +H FD Sbjct: 272 WAVTVETVELLGAERLIYGR-INGEQ--VIVRVEEGTHSPEPDSVIHVQPRADRLHAFDA 328 Query: 361 ETG 363 TG Sbjct: 329 ATG 331 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: 389 Number of extensions: 20 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: 334 Length adjustment: 29 Effective length of query: 354 Effective length of database: 305 Effective search space: 107970 Effective search space used: 107970 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 17 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