GapMind for catabolism of small carbon sources

 

Alignments for a candidate for patD in Desulfobacter vibrioformis DSM 8776

Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate WP_035239838.1 Q366_RS13505 NAD-dependent succinate-semialdehyde dehydrogenase

Query= BRENDA::G5DDC2
         (506 letters)



>NCBI__GCF_000745975.1:WP_035239838.1
          Length = 484

 Score =  303 bits (775), Expect = 1e-86
 Identities = 169/476 (35%), Positives = 264/476 (55%), Gaps = 10/476 (2%)

Query: 11  RQLFVDGEWRPPAQGRRLPVVNPTTEAHIGEIPAGTAEDVDAAVAAARAALKRNRGRDWA 70
           R  F+  EW     G+ + V NP T   +G +P   A++   A+ AA  +L       W 
Sbjct: 12  RHCFIQDEWVAADSGKTVDVTNPATGQILGTVPFCGADETQRAINAANESLDA-----WR 66

Query: 71  RAPGAVRAKYLRAIAAKVIERKQELAKLEALDCGKPYDEAAWDMDDVAGCFEYFADQAEA 130
                 R+  LR     ++E +++LA +   + GKP  E+  ++   A  FE+FA++A+ 
Sbjct: 67  SKTAGERSAILRKWYDLLMENQEDLAVIMTAEQGKPLAESRGEIAYAAAFFEWFAEEAKR 126

Query: 131 LDKRQNSPVSLPMETFKCHLRREPIGVVGLITPWNYPLLMATWKVAPALAAGCAAVLKPS 190
           +       +   + + +  + ++P+GVV  ITPWN+P  M T K   ALAAGC  VLKP+
Sbjct: 127 V---YGDVIPQTVASQRLVVIKQPVGVVAAITPWNFPSAMITRKAGAALAAGCTMVLKPA 183

Query: 191 ELASVTCLELADICKEVGLPPGVLNIVTGLGPDAGAPLSAHPDVDKVAFTGSFETGKKIM 250
                + L +A + ++ G+P GV N+VTG     G  L+A+P V K+ FTGS + GKK+M
Sbjct: 184 TATPFSALAIAKLGQQAGVPKGVFNVVTGSSSAIGGELTANPIVRKLTFTGSTQVGKKLM 243

Query: 251 AAAAPMVKPVTLELGGKSPIVVFDDVDIDKAVEWTLFGCFWTNGQICSATSRLLVHTKIA 310
              A  +K +++ELGG +P +VFDD DID AVE  +   +  +GQ C   +R+ V   + 
Sbjct: 244 RDCAGTMKRLSMELGGNAPFIVFDDADIDAAVEGAMACKYRNSGQTCVCANRMYVQAGVY 303

Query: 311 KEFNEKMVAWAKNIKVSDPLEEGCRLGPVVSEGQYEKIKKFILNAKSEGATILTGGVRPA 370
            EF  K+ A  + +KV +  ++G + GP++     E ++  I +A  +G  +L GG R A
Sbjct: 304 DEFCRKLTAAVQELKVGNGFDDGVQQGPLIDMAAVETVESHIKDAVDKGGKVLAGGTRHA 363

Query: 371 HLEKGFFIEPTIITDITTSMEIWREEVFGPVLCVKEFSTEDEAIELANDTQYGLAGAVIS 430
            L + FF  PTII D+T  M + REE FGP+  V +F TE+E +  ANDT++GLA    +
Sbjct: 364 -LGRTFF-APTIIADVTDDMRVAREETFGPLAPVFKFDTEEEVVRKANDTEFGLAAYFYT 421

Query: 431 GDRERCQRLSEEIDAGIIWVNCSQPCFCQAPWGGNKRSGFGRELGEGGIDNYLSVK 486
            D  R  R+ E+++ G++ +N        AP+GG K SG GRE  + G+D+YL +K
Sbjct: 422 RDMARSWRIGEKLEYGLVGINSGIISNPVAPFGGVKESGNGREGSKYGLDDYLEIK 477


Lambda     K      H
   0.318    0.135    0.421 

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: 585
Number of extensions: 31
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: 506
Length of database: 484
Length adjustment: 34
Effective length of query: 472
Effective length of database: 450
Effective search space:   212400
Effective search space used:   212400
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 Apr 09 2024. 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