GapMind for catabolism of small carbon sources

 

Aligments for a candidate for rocA in Marinobacter adhaerens HP15

Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate GFF4005 HP15_3945 aldehyde dehydrogenase family protein

Query= BRENDA::Q72IB9
         (516 letters)



>lcl|FitnessBrowser__Marino:GFF4005 HP15_3945 aldehyde dehydrogenase
           family protein
          Length = 471

 Score =  238 bits (607), Expect = 4e-67
 Identities = 161/477 (33%), Positives = 243/477 (50%), Gaps = 20/477 (4%)

Query: 41  YIGGEWVDTKERMVSLNPSAPSEVVGTTAKAGKAEAEAALEAAWKAFKTWKDWPQEDRSR 100
           YI G+WV     M+ ++ +   +V+     AG  E E A+ AA  AF++W +   E+R +
Sbjct: 8   YINGQWVSWAGDMIDVHEAGTGDVIARVPAAGADEMEQAIAAADAAFESWSESTLEERIK 67

Query: 101 LLLKAAALMRRRKRELEATLVYEVGKNWVEASADVAEAIDFIEYYARAALRYRYPAVEVV 160
           +L +  A ++ R  E+  T+  EVG   ++ +  +   +      +   L   +P  E  
Sbjct: 68  VLEQLHAGLKERAPEIAETVCREVGMP-IKLATPIQAGMPAAVTKSYLKLLPDFPFTE-- 124

Query: 161 PYPGEDNESFYVPLGAGVVIAPWNFPVAIFTGMIMGPVAVGNTVIAKPAEDAVVVGAKVF 220
                ++E  Y P+G    I PWN+P+      I+  +A G TV+ KP+E A      + 
Sbjct: 125 --QSGNSEVQYAPVGVVGCITPWNYPLHQVILKIVPAIAAGCTVVLKPSEIAPQTAFILA 182

Query: 221 EIFHEAGFPPGVVNFLPGVGEEVGAYLVEHPRTRFINFTGSLEVGLKIYEAAGRLAPGQT 280
           EI      P GV N + G G  VG  L++HP  R ++FTGS   G  I  AA        
Sbjct: 183 EILDGTDLPKGVFNMVCGYGHTVGDTLIKHPDVRMVSFTGSTRTGNLIAHAAA------D 236

Query: 281 WFKRAYVETGGKDAIIVDETADFDLAAEGVVVSAYGFQGQKCSAASRLILTQGAYEPVLE 340
            FKR  +E GGK A ++   AD   A +G + +     GQ C+A +R+++    ++   E
Sbjct: 237 DFKRFALEMGGKSASVILPDADLAAAVKGTINNCLLNSGQTCTALTRMLVPADKHDEACE 296

Query: 341 RVLKRAERLSVG-PAEENPDLGPVVSAEQERKVLSYIEIGKNEG-QLVLGGKRL-EG--E 395
                  +++ G P EE   LGP+ SA+Q  KV+ YI++G  EG +L+ GG    EG  +
Sbjct: 297 LAAAAVAKMTPGNPLEETTRLGPLSSAQQRDKVIDYIKLGVQEGAKLIAGGPEAPEGCEK 356

Query: 396 GYFIAPTVFTEVPPKARIAQEEIFGPVLSVIRVKDFAEALEVANDTPYGLTGGVYSRKRE 455
           GYF+  TVF  V P +RIAQEEIFGPVL VI   D AEA+++AN T YGL+G V+S    
Sbjct: 357 GYFVKATVFGNVKPDSRIAQEEIFGPVLCVIPYNDEAEAVKIANGTQYGLSGAVWSGDDA 416

Query: 456 HLEWARREFHVGNLYFNRKITGALVGVQPFGGFKLSGTNAKTGALDYLRLFLEMKAV 512
             +    +   G ++ N    GA   + PFGGF  SG   + G    L  FLE++++
Sbjct: 417 KAKKIASKLRTGQVFVN---GGAFNPMAPFGGFGHSGIGREFGKWG-LEEFLEVRSL 469


Lambda     K      H
   0.319    0.137    0.403 

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: 526
Number of extensions: 33
Number of successful extensions: 6
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: 516
Length of database: 471
Length adjustment: 34
Effective length of query: 482
Effective length of database: 437
Effective search space:   210634
Effective search space used:   210634
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 (21.7 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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