GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dctP in Photobacterium gaetbulicola Gung47

Align C4-dicarboxylate-binding periplasmic protein DctP (characterized, see rationale)
to candidate WP_044620695.1 H744_RS01505 TRAP transporter substrate-binding protein

Query= uniprot:I7END8
         (333 letters)



>NCBI__GCF_000940995.1:WP_044620695.1
          Length = 351

 Score =  147 bits (370), Expect = 5e-40
 Identities = 98/326 (30%), Positives = 167/326 (51%), Gaps = 11/326 (3%)

Query: 4   VTAAATAVALTMSAGTAMAACDDGEIVVKFSHVTNTDKHPKGIAASLLEKRINEEMNGTM 63
           +  AA       +  T   AC+     ++FS  +NT +HP    AS  ++ +  E    +
Sbjct: 18  IIGAAIVTNGNNTTNTTNLACESQIKTLRFSMSSNT-QHPIYDGASKFKELV--EKTTDL 74

Query: 64  CLEVYPNSTLYNDNKVLEAMLQGDVQLAAPSLSKFEKFTKQFRLFDLPFMFKNIDAVDAF 123
            +++YP++ L +D   +E +  G + ++ PS +    F  ++ +FDLPFM  N    D  
Sbjct: 75  TVDIYPSAQLGDDRAAIEMLQLGTLDVSIPSTAPLANFYPEYNVFDLPFMIPNEAVADKV 134

Query: 124 QGSENGQAMLDSMQRRGLQGLSYWHNGMKQMS-ANKPLINPSDANGLKFRVQSSDVLVAQ 182
             S+    ML+ +Q R L GL +W NG + ++ + + + +  D  GLK R   S + +  
Sbjct: 135 LRSDFAGDMLEMLQSRRLIGLDFWENGFRHLTNSRRTVTSVDDVKGLKVRTMESPLHLDA 194

Query: 183 MEAIGGSPQKMAFSEVYGALQQGVVDGQENTWSNIYGKKFFEVQDGVTETNHGALD-YLV 241
            +A+G +P  MAF+E++ ALQQG VDGQEN + NI     +EVQ  +T+T H      L+
Sbjct: 195 WKALGATPTPMAFNELFTALQQGTVDGQENPYPNIALNNLYEVQKQMTDTGHVYTPLVLI 254

Query: 242 VTSVDW--LDSLDPAVREQFLTILGEVTATRNSESTKVNAEARQSIIDAGGVVRELTPEQ 299
            +   W  L + D A   Q     G+    +   + +VN ++  + I A   V ELTPE 
Sbjct: 255 FSEASWNKLSAHDQAAVRQAAIEAGDY---QREVNRRVNNDS-LATIKANMQVTELTPEA 310

Query: 300 RAAWVEAMKPVWEQFAGDVGQDMIDA 325
           R+ + +A + V +++   +G D+ID+
Sbjct: 311 RSEFRKATESVVDKYRDVIGGDIIDS 336


Lambda     K      H
   0.316    0.130    0.371 

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: 278
Number of extensions: 19
Number of successful extensions: 4
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: 333
Length of database: 351
Length adjustment: 29
Effective length of query: 304
Effective length of database: 322
Effective search space:    97888
Effective search space used:    97888
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: 41 (21.6 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Sep 24 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