GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xacK in Shewanella loihica PV-4

Align Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale)
to candidate 5208351 Shew_0863 ABC transporter-related protein (RefSeq)

Query= uniprot:D4GP39
         (383 letters)



>FitnessBrowser__PV4:5208351
          Length = 342

 Score =  179 bits (453), Expect = 1e-49
 Identities = 94/246 (38%), Positives = 155/246 (63%), Gaps = 12/246 (4%)

Query: 1   MARLTLDDVTKVYTDEGGGDIVAVEEISLDIDDGEFLVLVGPSGCGKSTTLRMMAGLETV 60
           M+ LT++   +V++D  G  I+    + L +  GE   L+GPSGCGK+T L+ +AGL+ +
Sbjct: 1   MSTLTIE---QVHSDYQGQTIL--RGLDLVLHQGEIAALLGPSGCGKTTLLKAIAGLQPI 55

Query: 61  TEGELRLEDRVLNG----VSAQDRDIAMVFQSYALYPHKSVRGNMSFGLEESTGLPDDEI 116
           ++G + +  R+L+G    V ++ R++ M+FQ YAL+PH +V  N+ FG++   GL     
Sbjct: 56  SQGRISINGRLLSGPETFVPSERREVGMIFQDYALFPHLTVAENILFGVK---GLDKAAR 112

Query: 117 RQRVEETTDMLGISDLLDRKPGQLSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRA 176
           + R+ E   ++ +  L  R P +LSGGQQQRV++ RA+  +PE+ L+DEP SN+DAK+R 
Sbjct: 113 QARLGEMLALVKLEGLGGRYPHELSGGQQQRVSIARALAYEPELLLLDEPFSNIDAKVRG 172

Query: 177 EMRTELQRLQGELGVTTVYVTHDQTEAMTMGDRVAVLDDGELQQVGTPLDCYHRPNNLFV 236
           EM  E++ +  + GV+ V+VTH + EA    D++A+  DG + Q G+    Y  P + +V
Sbjct: 173 EMMVEIREILKQRGVSAVFVTHSKDEAFVFADKLALFKDGGIAQYGSAESLYAEPTDKYV 232

Query: 237 AGFIGE 242
           A F+G+
Sbjct: 233 AEFLGQ 238


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: 352
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: 342
Length adjustment: 29
Effective length of query: 354
Effective length of database: 313
Effective search space:   110802
Effective search space used:   110802
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