GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xacK in Phaeobacter inhibens BS107

Align Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale)
to candidate GFF1645 PGA1_c16680 sugar ABC transporter, ATP-binding protein

Query= uniprot:D4GP39
         (383 letters)



>FitnessBrowser__Phaeo:GFF1645
          Length = 355

 Score =  298 bits (764), Expect = 1e-85
 Identities = 177/369 (47%), Positives = 229/369 (62%), Gaps = 19/369 (5%)

Query: 1   MARLTLDDVTKVYTDEGGGDIVAVEEISLDIDDGEFLVLVGPSGCGKSTTLRMMAGLETV 60
           MAR+ L DV K Y     G +  + +I+LDI DGEF+VLVGPSGCGKST LRM+AGLE +
Sbjct: 1   MARIELRDVAKRY-----GAVEVLRDINLDIQDGEFIVLVGPSGCGKSTLLRMIAGLEPI 55

Query: 61  TEGELRLEDRVLNGVSAQDRDIAMVFQSYALYPHKSVRGNMSFGLEESTGLPDDEIRQRV 120
           T G+  ++ + +N V  +DRDIAMVFQSYALYPH  V  NM F +E     P +E R RV
Sbjct: 56  TSGDFEIDGQRMNDVRPRDRDIAMVFQSYALYPHMDVARNMGFSMEIRKD-PAEERRSRV 114

Query: 121 EETTDMLGISDLLDRKPGQLSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRT 180
               + LG+S L+DR P  LSGGQ+QRVA+GRAI+RDP  FL DEPLSNLDA LR EMR 
Sbjct: 115 ARAAETLGLSSLVDRLPKALSGGQRQRVAMGRAIIRDPRAFLFDEPLSNLDAALRVEMRL 174

Query: 181 ELQRLQGELGVTTVYVTHDQTEAMTMGDRVAVLDDGELQQVGTPLDCYHRPNNLFVAGFI 240
           E+ RL  +LG T +YVTHDQ EA+T+ DR+ VL+ G++QQVG+PL+ Y RP N FVA FI
Sbjct: 175 EIARLHKQLGATMIYVTHDQVEALTLADRIVVLNGGDIQQVGSPLELYERPANKFVAQFI 234

Query: 241 GEPSMNLF--DGSLSGDTFRGDGFDYPLSGATRDQLGGASGLTLGIRPEDVTVGERRSGQ 298
           G P+MN+    G+ SG     +G    L          A+ + LGIRPE + V E   G 
Sbjct: 235 GSPTMNILPVSGAASG-VMATNGMMLTLD----HMHDTAAAVELGIRPEHLDVVEPGEGH 289

Query: 299 RTFDAEVVVVEPQGNENAVHLRFVDGDEGTQFTATTTGQSRVEAGDRTTVSFPEDAIHLF 358
               A+  VVE  G++  ++ + VDG           G   V +G+R  +       H+F
Sbjct: 290 LIAVAD--VVERLGSDTNIYAK-VDG--LGPLMVRKHGNVPVRSGERLGLRVQAQNAHIF 344

Query: 359 DGETGDALK 367
           D + G AL+
Sbjct: 345 D-DRGIALR 352


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: 408
Number of extensions: 18
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: 355
Length adjustment: 30
Effective length of query: 353
Effective length of database: 325
Effective search space:   114725
Effective search space used:   114725
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.

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About GapMind

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:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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