Align Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale)
to candidate RR42_RS12955 RR42_RS12955 glycerol-3-phosphate ABC transporter ATP-binding protein
Query= uniprot:D4GP39 (383 letters) >FitnessBrowser__Cup4G11:RR42_RS12955 Length = 367 Score = 285 bits (729), Expect = 1e-81 Identities = 170/383 (44%), Positives = 235/383 (61%), Gaps = 33/383 (8%) Query: 1 MARLTLDDVTKVYTDEGGGDIVAVEEISLDIDDGEFLVLVGPSGCGKSTTLRMMAGLETV 60 MA+L+L +V K Y G++ V I ++I+DGEF+V+VGPSGCGKST LRM+AGLE + Sbjct: 1 MAKLSLRNVQKTYA----GNVKVVHGIDMEINDGEFIVIVGPSGCGKSTLLRMVAGLEAI 56 Query: 61 TEGELRLEDRVLNGVSAQDRDIAMVFQSYALYPHKSVRGNMSFGLEESTGLPDDEIRQRV 120 + GE+ + D+V+N + +RDIAMVFQ+YALYPH SV NM++GL+ G+ EI QRV Sbjct: 57 SGGEVHIGDKVVNHLEPAERDIAMVFQNYALYPHMSVYDNMAYGLK-IRGMDKSEIEQRV 115 Query: 121 EETTDMLGISDLLDRKPGQLSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRT 180 + +L ++ LL+RKP LSGGQ+QRVA+GRAIVR+P VFL DEPLSNLDAKLR +MR Sbjct: 116 KHAAGILELAPLLERKPRALSGGQRQRVAMGRAIVREPAVFLFDEPLSNLDAKLRVQMRL 175 Query: 181 ELQRLQGELGVTTVYVTHDQTEAMTMGDRVAVLDDGELQQVGTPLDCYHRPNNLFVAGFI 240 EL+ L L T++YVTHDQ EAMT+ DR+ VL+ G ++Q+GTPL+ Y RP + FVA FI Sbjct: 176 ELKELHRRLRTTSMYVTHDQVEAMTLADRMMVLNGGSVEQIGTPLEVYARPASTFVASFI 235 Query: 241 GEPSMNLFDGSLSGDTFRGDGFDYPLSGATRDQLGGASG--LTLGIRPEDVTVGER---- 294 G P MNL + T G G + +Q GA G TLG P + + ER Sbjct: 236 GSPPMNLVPVT---RTNGGQG----EAQMRVEQKPGAQGAPATLGHLPMGLHLPERALLG 288 Query: 295 ---------RSGQRTFDAEVVVVEPQGNENAVHLRFVDGDEGTQ-FTATTTGQSRVEAGD 344 + + + EV +VE G ++ + G G Q V +GD Sbjct: 289 LRPEHIEPCAAHEAIAEIEVRLVEALGADS-----YAYGTLGGQPVVVRLDSNMPVSSGD 343 Query: 345 RTTVSFPEDAIHLFDGETGDALK 367 R ++ + +H FD ++G ++ Sbjct: 344 RLPITAAAEHLHFFDADSGKRIE 366 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: 434 Number of extensions: 25 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: 367 Length adjustment: 30 Effective length of query: 353 Effective length of database: 337 Effective search space: 118961 Effective search space used: 118961 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: 50 (23.9 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