Align Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale)
to candidate 3608008 Dshi_1416 ABC transporter related (RefSeq)
Query= uniprot:D4GP39 (383 letters) >FitnessBrowser__Dino:3608008 Length = 347 Score = 296 bits (757), Expect = 8e-85 Identities = 172/363 (47%), Positives = 222/363 (61%), Gaps = 19/363 (5%) Query: 1 MARLTLDDVTKVYTDEGGGDIVAVEEISLDIDDGEFLVLVGPSGCGKSTTLRMMAGLETV 60 MA + L+ V K + G V VE+ L I D EFLVL+GPSGCGK+TT+RM+AGLE Sbjct: 1 MAEIRLNHVQKRW-----GSFVGVEDFHLTIPDREFLVLLGPSGCGKTTTMRMIAGLEEP 55 Query: 61 TEGELRLEDRVLNGVSAQDRDIAMVFQSYALYPHKSVRGNMSFGLEESTGLPDDEIRQRV 120 + GE+ + DR++N + +DRD+AMVFQSY LYP+ +V N+ F L+ +P+ E RV Sbjct: 56 SSGEIWIGDRMVNALDPKDRDVAMVFQSYGLYPNMNVYENIRFPLKVRK-VPEVEHEARV 114 Query: 121 EETTDMLGISDLLDRKPGQLSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRT 180 + M+ + D L RKP LSGGQ+QRVAL RAIVR+P VFLMDEPLSNLDAKLR R Sbjct: 115 MRASAMVELDDFLHRKPAALSGGQRQRVALARAIVREPNVFLMDEPLSNLDAKLRVSTRA 174 Query: 181 ELQRLQGELGVTTVYVTHDQTEAMTMGDRVAVLDDGELQQVGTPLDCYHRPNNLFVAGFI 240 +++ L EL VTT+YVTHDQ EAMT+ DRV V+ G +QQVGTP++ Y RP N FVA FI Sbjct: 175 QIKNLSHELQVTTIYVTHDQIEAMTLADRVVVMSAGVVQQVGTPMEIYDRPANTFVASFI 234 Query: 241 GEPSMNLFDGSLSGDTFRGDGFDYPLSGATRDQLGGASGLTLGIRPEDVTVGERRSGQRT 300 G P+MNL +G+++ TF GD A G A +TLG R ED V + GQ Sbjct: 235 GSPAMNLMEGAVTDGTFHGDRV------AIAGLSGAAGRVTLGFRAEDAQVVD-SDGQ-- 285 Query: 301 FDAEVVVVEPQGNENAVHLRFVDGDEGTQFTATTTGQSRVEAGDRTTVSFPEDAIHLFDG 360 A V +E G+ V ++ GT + R E G + P HLFD Sbjct: 286 IAAPVYSMELLGDATMVTVK----AGGTLVAVKAPKEFRAEIGAPVQIRIPTGICHLFDA 341 Query: 361 ETG 363 +TG Sbjct: 342 QTG 344 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: 433 Number of extensions: 17 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: 347 Length adjustment: 29 Effective length of query: 354 Effective length of database: 318 Effective search space: 112572 Effective search space used: 112572 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