GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xacK in Shewanella oneidensis MR-1

Align Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale)
to candidate 202699 SO3602 sulfate ABC transporter, ATP-binding protein (NCBI ptt file)

Query= uniprot:D4GP39
         (383 letters)



>FitnessBrowser__MR1:202699
          Length = 376

 Score =  214 bits (544), Expect = 4e-60
 Identities = 129/357 (36%), Positives = 196/357 (54%), Gaps = 12/357 (3%)

Query: 19  GDIVAVEEISLDIDDGEFLVLVGPSGCGKSTTLRMMAGLETVTEGELRLEDRVLNGVSAQ 78
           G   A+  ++LDI +GE + L+GPSG GK+T LR++AGLE    G +   +R +  V  +
Sbjct: 13  GQFQALSPLNLDIQEGEMIGLLGPSGSGKTTLLRIIAGLEGADSGHIHFGNRDVTQVHVR 72

Query: 79  DRDIAMVFQSYALYPHKSVRGNMSFGLE---ESTGLPDDEIRQRVEETTDMLGISDLLDR 135
           DR +  VFQ+YAL+ H +V  N++FGLE   +       EI++RV    +M+ +  L  R
Sbjct: 73  DRRVGFVFQNYALFRHMTVADNVAFGLEVIPKKQRPSAAEIQKRVSHLLEMVQLGHLAQR 132

Query: 136 KPGQLSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRTELQRLQGELGVTTVY 195
            P QLSGGQ+QR+AL RA+   PEV L+DEP   LDAK+R E+R  L+ L  EL  T+V+
Sbjct: 133 YPEQLSGGQKQRIALARALATQPEVLLLDEPFGALDAKVRKELRRWLRSLHDELKFTSVF 192

Query: 196 VTHDQTEAMTMGDRVAVLDDGELQQVGTPLDCYHRPNNLFVAGFIGEPSMNLFDGSLSGD 255
           VTHDQ EA+ + DRV V+ +G ++QV TP++ Y +PN+ FV  F+G  ++N F+ +   +
Sbjct: 193 VTHDQDEALELSDRVVVMSNGNIEQVNTPIELYAQPNSRFVFDFLG--NVNRFEANWQQN 250

Query: 256 TF-RGDGFDYPLSGATRDQLGGASGLTLGIRPEDVTVGERRSGQRTFDAEVVVVEPQGNE 314
            +  GD F  P       Q G      L +R  ++ + ++ + Q      +V + P G E
Sbjct: 251 RWTNGDAFIVPPEQTPLQQNG-----ALYVRSHELALADKPNSQAHIPFTIVAITPIGAE 305

Query: 315 NAVHLRFVDGDEGTQFTATTTGQSRVEAG-DRTTVSFPEDAIHLFDGETGDALKNRE 370
             V L  +       + A  T     E G  + +V +       F G+ GD    R+
Sbjct: 306 VRVELAPIGWQSEELWEAKFTHHHLQELGLQKGSVVYATPRTGYFFGKQGDGSPIRQ 362


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: 379
Number of extensions: 21
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: 376
Length adjustment: 30
Effective length of query: 353
Effective length of database: 346
Effective search space:   122138
Effective search space used:   122138
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