GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gabD in Caulobacter crescentus NA1000

Align Succinate-semialdehyde dehydrogenase, mitochondrial; At-SSADH1; Aldehyde dehydrogenase family 5 member F1; NAD(+)-dependent succinic semialdehyde dehydrogenase; Protein ENLARGED FIL EXPRESSING DOMAIN 1; EC 1.2.1.24 (characterized)
to candidate CCNA_00424 CCNA_00424 aldehyde dehydrogenase

Query= SwissProt::Q9SAK4
         (528 letters)



>FitnessBrowser__Caulo:CCNA_00424
          Length = 479

 Score =  284 bits (726), Expect = 6e-81
 Identities = 170/479 (35%), Positives = 256/479 (53%), Gaps = 25/479 (5%)

Query: 53  TQGLIGGKWLDSYDNKTIKVNNPATGEIIADVACMGTKETNDAIASSYEAFTSWSRLTAG 112
           T+  I G W+D     T+ V NPAT E+   ++     + + A+ ++ +AF S+S+ +  
Sbjct: 5   TKFYIDGAWVDPAAPNTLDVINPATEEVCGVISMGSEADVDKAVRAARKAFASFSQTSRE 64

Query: 113 ERSKVL--------RRWYDLLIAHKEELGQLITLEQGKPLKEAIGEVAYGASFIEYYAEE 164
           ER  +L        +R+ D+  A  EE+G    L Q       IG V   A+ ++ Y  E
Sbjct: 65  ERIDILERIIAEYQKRFEDMAKAITEEMGAPAWLAQRAQAAMGIGHVQTAAAVLKGYKFE 124

Query: 165 AKRVYGDIIPPNLSDRRLLVLKQPVGVVGAITPWNFPLAMITRKVGPALASGCTVVVKPS 224
             R    I+            K+P+GV   ITPWN+P+  I  KVGPA+A+GCT+V+KPS
Sbjct: 125 EDRGTTRIV------------KEPIGVCAFITPWNWPVNQIACKVGPAIATGCTMVLKPS 172

Query: 225 ELTPLTALAAAELALQAGVPPGALNVVMGNAPEIGDALLTSPQVRKITFTGSTAVGKKLM 284
           E+ P +     E+   AGVP G  N+V G+ P +G AL   P+V  ++FTGST  G ++ 
Sbjct: 173 EIAPFSGYIWTEIMHAAGVPAGVFNLVNGDGPTVGAALSRHPEVDMVSFTGSTRAGIEVA 232

Query: 285 AAAAPTVKKVSLELGGNAPSIVFDDADLDVAVKGTLAAKFRNSGQTCVCANRVLVQDGIY 344
             AAPTVK+V  ELGG +P+I+ DDAD   AV G +A+   NSGQ+C    R+LV     
Sbjct: 233 KNAAPTVKRVHQELGGKSPNIILDDADFSRAVAGGVASVMMNSGQSCNAPTRMLVPGARM 292

Query: 345 DKFAEAFSEAVQKLEVGDGFRDGTTQGPLINDAAVQKVETFVQDAVSKGAKIIIGGKRHS 404
           D+       A +   VGD        GP++++    K++  +Q  + +GA ++ GG    
Sbjct: 293 DEVIAIAKAAAESHTVGDP-NGNHKMGPVVSETQWNKIQGLIQKGIDEGATLVTGGVGRP 351

Query: 405 LGMT---FYEPTVIRDVSDNMIMSKEEIFGPVAPLIRFKTEEDAIRIANDTIAGLAAYIF 461
            G+    + +PTV  +V++ M ++KEEIFGPV  ++ + T ++A+ + NDT  GLAAY+ 
Sbjct: 352 EGLDKGYYVKPTVFANVTNEMTIAKEEIFGPVVSILGYDTVDEAVTVGNDTEYGLAAYVS 411

Query: 462 TNSVQRSWRVFEALEYGLVGVNEGLISTEVAPFGGVKQSGLGREGSKYGMDEYLEIKYV 520
                   +V   L  G V +N G     +APFGG K SG GRE   +   E+LE K +
Sbjct: 412 GGDQDEVRKVASRLRAGQVTLN-GAGPDLMAPFGGYKMSGNGREWGDHAFGEFLETKAI 469


Lambda     K      H
   0.317    0.134    0.383 

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: 551
Number of extensions: 19
Number of successful extensions: 5
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: 528
Length of database: 479
Length adjustment: 34
Effective length of query: 494
Effective length of database: 445
Effective search space:   219830
Effective search space used:   219830
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 (21.7 bits)
S2: 52 (24.6 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