GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xacK in Pseudomonas stutzeri RCH2

Align Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale)
to candidate GFF857 Psest_0871 ABC-type sugar transport systems, ATPase components

Query= uniprot:D4GP39
         (383 letters)



>FitnessBrowser__psRCH2:GFF857
          Length = 371

 Score =  285 bits (728), Expect = 2e-81
 Identities = 168/373 (45%), Positives = 225/373 (60%), Gaps = 22/373 (5%)

Query: 1   MARLTLDDVTKVYTDEGGGDIVAVEEISLDIDDGEFLVLVGPSGCGKSTTLRMMAGLETV 60
           MA +TL D+ K Y    G  I     I LDI+DGEF+V VGPSGCGKST LR++AGLE +
Sbjct: 1   MASVTLRDICKSYD---GTPIT--RHIDLDIEDGEFVVFVGPSGCGKSTLLRLIAGLEDI 55

Query: 61  TEGELRLEDRVLNGVSAQDRDIAMVFQSYALYPHKSVRGNMSFGLEESTGLPDDEIRQRV 120
           T G+L ++++ +N +  +DR + MVFQSYALYPH +V  NM+FGL+ ++ +   EI++RV
Sbjct: 56  TSGDLLIDNQRVNDLPPKDRSVGMVFQSYALYPHMTVAENMAFGLKLAS-VDKREIKRRV 114

Query: 121 EETTDMLGISDLLDRKPGQLSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRT 180
           E   ++L +  LL+RKP  LSGGQ+QRVA+GR +VR+P+VFL DEPLSNLDA LR +MR 
Sbjct: 115 EAVAEILQLDKLLERKPKDLSGGQRQRVAIGRTMVREPKVFLFDEPLSNLDAFLRVQMRI 174

Query: 181 ELQRLQGELGVTTVYVTHDQTEAMTMGDRVAVLDDGELQQVGTPLDCYHRPNNLFVAGFI 240
           E+ RL   +  T +YVTHDQ EAMT+ D++ VL+ GE+ QVG PL  YH P N FVAGF+
Sbjct: 175 EIARLHQRIRSTMIYVTHDQVEAMTLADKIVVLNAGEIAQVGQPLHLYHYPKNRFVAGFL 234

Query: 241 GEPSMNLFDG---SLSGDTF-----RGDGFDYPLSGATRDQLGGASGLTLGIRPEDVTVG 292
           G P MN  +    S S +T       G     P+ G+    +     LTLGIRPE   + 
Sbjct: 235 GSPQMNFVEVRAISASPETVTIELPSGYPLTLPVDGSA---VSPGDPLTLGIRPEHFVMP 291

Query: 293 ERRSGQRTFDAEVVVVEPQGNENAVHLRFVDGDEGTQFTATTTGQSRVEAGDRTTVSFPE 352
           +      TF  ++ V E  G  N ++L      +    T    G  RV  G+        
Sbjct: 292 D--EADFTFHGQITVAERLGQYNLLYLTLERLQD--VITLCVDGNLRVTEGETFAAGLKA 347

Query: 353 DAIHLFDGETGDA 365
           D  HLF  E G+A
Sbjct: 348 DKCHLF-RENGEA 359


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: 463
Number of extensions: 30
Number of successful extensions: 2
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: 371
Length adjustment: 30
Effective length of query: 353
Effective length of database: 341
Effective search space:   120373
Effective search space used:   120373
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.

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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