Align Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale)
to candidate AZOBR_RS25595 AZOBR_RS25595 sugar ABC transporter ATP-binding protein
Query= uniprot:D4GP39 (383 letters) >FitnessBrowser__azobra:AZOBR_RS25595 Length = 358 Score = 284 bits (727), Expect = 2e-81 Identities = 170/371 (45%), Positives = 220/371 (59%), Gaps = 25/371 (6%) Query: 1 MARLTLDDVTKVYTDEGGGDIVAVEEISLDIDDGEFLVLVGPSGCGKSTTLRMMAGLETV 60 MA +TL V K + G I + + L++ DGEF+ VGPSGCGKST LR++AGLE Sbjct: 1 MAGVTLRGVRKSF-----GRIEVIHGVDLEVADGEFVAFVGPSGCGKSTLLRLIAGLEEP 55 Query: 61 TEGELRLEDRVLNGVSAQDRDIAMVFQSYALYPHKSVRGNMSFGLEESTGLPDDEIRQRV 120 + G+L + + +N R IAMVFQSYALYPH + NM+FGL S I +RV Sbjct: 56 SGGDLSIGGQRVNDRPPAARGIAMVFQSYALYPHMTAYDNMAFGLTLSR-TDKGTIAERV 114 Query: 121 EETTDMLGISDLLDRKPGQLSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRT 180 +L I DLLDRKP LSGGQ+QRVA+GRAIVR+P+VFL DEPLSNLDA LR +MR Sbjct: 115 RAAARLLQIEDLLDRKPRDLSGGQRQRVAIGRAIVREPQVFLFDEPLSNLDAGLRVQMRL 174 Query: 181 ELQRLQGELGVTTVYVTHDQTEAMTMGDRVAVLDDGELQQVGTPLDCYHRPNNLFVAGFI 240 E+ +L+ +L T +YVTHDQ EAMT+ DR+ VL+ G ++Q GTPL+ YHRP N FVAGFI Sbjct: 175 EIAKLKADLRATMIYVTHDQVEAMTLADRIVVLNAGRVEQAGTPLELYHRPRNRFVAGFI 234 Query: 241 GEPSMN--------LFDGSLSGDTFRGDGFDYPLSGATRDQLGGASGLTLGIRPEDVTVG 292 G P+MN L DGS+ G D + GA + LTLG+RPE V + Sbjct: 235 GSPAMNFLDVVSEGLTDGSVRVWLPGGVPLDIAVDGAAP---AAGTPLTLGVRPEHVGLA 291 Query: 293 ERRSGQRTFDAEVVVVEPQGNENAVHLRFVDGDEGTQFTATTTGQSRVEAGDRTTVSFPE 352 + +G A ++ VE G E H DG + G V AG+R ++ Sbjct: 292 DGGAG---LLATILAVERLGGETHCHAALEDGQ---RLLVRLDGDRPVAAGERLRLNLRG 345 Query: 353 DAIHLF--DGE 361 + HLF DG+ Sbjct: 346 ETAHLFGPDGQ 356 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: 503 Number of extensions: 35 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: 358 Length adjustment: 30 Effective length of query: 353 Effective length of database: 328 Effective search space: 115784 Effective search space used: 115784 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