GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gabD in Moritella dasanensis ArB 0140

Align succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79); glyceraldehyde-3-phosphate dehydrogenase (NADP+) (EC 1.2.1.9) (characterized)
to candidate WP_017222570.1 A923_RS0115365 bifunctional proline dehydrogenase/L-glutamate gamma-semialdehyde dehydrogenase PutA

Query= BRENDA::Q97XA5
         (470 letters)



>NCBI__GCF_000276805.1:WP_017222570.1
          Length = 1038

 Score =  161 bits (407), Expect = 1e-43
 Identities = 137/457 (29%), Positives = 211/457 (46%), Gaps = 34/457 (7%)

Query: 9    VRSPSNLKV-IGTVKRMSKDEVRGEIEEAYKGFEIISRMPLYKRTAILRKISEILEREQE 67
            V +P + ++ +G V   +  EV   ++ A   F   S +P+ +R A L  I+++LE    
Sbjct: 580  VSAPYDRRIHVGQVLWSTPAEVTTALDTAADYFPTWSAVPVAERAACLNNIADLLEENLA 639

Query: 68   RLARLLAMEAGKPISDSRVEVLRASRLFR----QAAEEVGIVLEGKNYRVDAYEYPPGNE 123
             L  L   EAGK I DS  EV  A    R    QA E   +      +   A +      
Sbjct: 640  ELVALCHKEAGKTIHDSLDEVREAVDFCRYYAMQATENFSVAKNQVRFDGIAQQV----- 694

Query: 124  NRIVLSTREPIGVVTAILPFNFPINSFAHKVAPALAVGNSVVVKPSINTPLAAVEMKKIL 183
                  TR+  GV   I P+NFP+  F  +VA AL  GN+V+ KP+  T L A    +++
Sbjct: 695  ------TRQGQGVFVCISPWNFPLAIFLGQVAAALVAGNTVIAKPAEQTSLIAARTMELM 748

Query: 184  VEAGLPDSAVRVVTGYSSEIGDEIITHPLVGLITLTGSTQTGLKIASKAISLGKR----- 238
            +EAG P  A+ ++ G  + +G  +     +  +  TGST+T   I     SL KR     
Sbjct: 749  LEAGFPKEAIHLLPGSGAVVGSLLTADERIAGVVFTGSTETAQVINR---SLAKRDTNVA 805

Query: 239  -IIMELGGSDPIIILEDANIERASSIAVRARFEYAGQNCNAGKRIIVRQEVYDKFVKAFN 297
             +I E GG + +I+   A  E+     +R+ F  AGQ C+A + + V+++V D+      
Sbjct: 806  TLIAETGGQNTMIVDSTALPEQVVRDVMRSAFASAGQRCSALRVLFVQEDVADRITTLIQ 865

Query: 298  EKAKALKVGEPLDETTDVGPVINKESVENLNSVLEDAKVKGGRVEILNRGPES--GSFF- 354
               K L VG P    TDVGPVI+  +   L + ++  +     V  +    E   G F  
Sbjct: 866  GAMKELHVGLPQQHHTDVGPVIDLLAKNKLQAHIDIMRATSKLVGEVTLSEECNFGDFIA 925

Query: 355  PLTMVTNPSLDMLVLKSEVFGPIVPIVSVKSDE--EAIRIANSTEYGLQSAIFTNDVNRA 412
            P+    N S+D   L++E FGPI+ IV  K+ E  + I   N+T +GL   I + +    
Sbjct: 926  PIAFEIN-SIDQ--LENEQFGPILHIVRYKAAELNKVISEINATGFGLTMGIHSRNERTY 982

Query: 413  LKLSRELKFGAVIIN-DSTRLRWDSLPFGGFKKTGIG 448
              + R+++ G   IN D         PFGG   +G G
Sbjct: 983  TDIERQIRVGNCYINRDQVGAVVGVQPFGGQGLSGTG 1019


Lambda     K      H
   0.316    0.135    0.366 

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: 875
Number of extensions: 44
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: 470
Length of database: 1038
Length adjustment: 39
Effective length of query: 431
Effective length of database: 999
Effective search space:   430569
Effective search space used:   430569
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: 54 (25.4 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