GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glpT in Shewanella sp. ANA-3

Align ABC transporter for Glycerol, ATPase component 2 (characterized)
to candidate 7026050 Shewana3_3192 sulfate ABC transporter, ATPase subunit (RefSeq)

Query= reanno::acidovorax_3H11:Ac3H11_792
         (358 letters)



>FitnessBrowser__ANA3:7026050
          Length = 376

 Score =  158 bits (399), Expect = 3e-43
 Identities = 104/292 (35%), Positives = 160/292 (54%), Gaps = 11/292 (3%)

Query: 23  ALLPLKMEFEDGGAYALLGPSGCGKTTMLNIMSGLLVPSHGKVLFDGRDVTRASPQERNI 82
           AL PL ++ ++G    LLGPSG GKTT+L I++GL     G++ F  RDVT+   ++R +
Sbjct: 17  ALSPLNLDIQEGEMIGLLGPSGSGKTTLLRIIAGLEGADSGQIHFGNRDVTQVHVRDRRV 76

Query: 83  AQVFQFPVIYDTMTVAENLAFPL----RNRKVPEGQIKQRVGVIAEMLEMSGQLNQRAAG 138
             VFQ   ++  MTVA+N+AF L    + ++  + +I++RV  + EM+++     +    
Sbjct: 77  GFVFQNYALFRHMTVADNVAFGLEVIPKKQRPSKAEIQKRVSHLLEMVQLGHLAQRYPEQ 136

Query: 139 LAADAKQKISLGRGLVRADVAAVLFDEPLTVIDPHLKWQLRRKLKQIHHELKLTLIYVTH 198
           L+   KQ+I+L R L       +L DEP   +D  ++ +LRR L+ +H ELK T ++VTH
Sbjct: 137 LSGGQKQRIALARALA-TQPEVLLLDEPFGALDAKVRKELRRWLRSLHDELKFTSVFVTH 195

Query: 199 DQVEALTFADQVVVMTRGKAVQVGSADALFERPAHTFVGHFIGSPGMNFLPAHRDGENLS 258
           DQ EAL  +D+VVVM+ G   QV +   L+ +P   FV  F+G+  +N   A       +
Sbjct: 196 DQDEALELSDRVVVMSNGNIEQVNTPIELYAQPNSRFVFDFLGN--VNRFEASWQQNRWT 253

Query: 259 VAGHRLASPVGRALPA-GALQVGIRPEYLALA-QPQQAGALPGTVVQVQDIG 308
                L  P    L   GAL V  R   LALA +P     +P T+V +  +G
Sbjct: 254 NGDAFLVPPEQTPLQQNGALYV--RSHELALADKPNSQAHIPFTIVAITPVG 303


Lambda     K      H
   0.320    0.136    0.395 

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: 306
Number of extensions: 9
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: 358
Length of database: 376
Length adjustment: 30
Effective length of query: 328
Effective length of database: 346
Effective search space:   113488
Effective search space used:   113488
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 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