GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nbaE in Desulfobacter vibrioformis DSM 8776

Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate WP_035239838.1 Q366_RS13505 NAD-dependent succinate-semialdehyde dehydrogenase

Query= BRENDA::Q8BH00
         (487 letters)



>NCBI__GCF_000745975.1:WP_035239838.1
          Length = 484

 Score =  300 bits (767), Expect = 1e-85
 Identities = 163/458 (35%), Positives = 257/458 (56%), Gaps = 10/458 (2%)

Query: 25  IDSYDPSTGEVYCKVPNSGKEEIEAAVEAAREAFPAWSSRSPQERSLVLNRLADVLEQSL 84
           +D  +P+TG++   VP  G +E + A+ AA E+  AW S++  ERS +L +  D+L ++ 
Sbjct: 29  VDVTNPATGQILGTVPFCGADETQRAINAANESLDAWRSKTAGERSAILRKWYDLLMENQ 88

Query: 85  EELAQAESKDQGKTLTLARTMDIPRSVLNFRFFASSNLHHVSECTQMSHLGCMHYTVRTP 144
           E+LA   + +QGK L  +R  +I  +   F +FA        +    +        ++ P
Sbjct: 89  EDLAVIMTAEQGKPLAESRG-EIAYAAAFFEWFAEEAKRVYGDVIPQTVASQRLVVIKQP 147

Query: 145 VGIAGLISPWNLPLYLLTWKIAPAIAAGNTVIAKPSEMTSVTAWMFCKLLDKAGVPPGVI 204
           VG+   I+PWN P  ++T K   A+AAG T++ KP+  T  +A    KL  +AGVP GV 
Sbjct: 148 VGVVAAITPWNFPSAMITRKAGAALAAGCTMVLKPATATPFSALAIAKLGQQAGVPKGVF 207

Query: 205 NIVFGTGPRVGEALVSHPEVPLISFTGSQPTAERITQLSAPHCKKLSLELGGKNPAIIFE 264
           N+V G+   +G  L ++P V  ++FTGS    +++ +  A   K+LS+ELGG  P I+F+
Sbjct: 208 NVVTGSSSAIGGELTANPIVRKLTFTGSTQVGKKLMRDCAGTMKRLSMELGGNAPFIVFD 267

Query: 265 DANLEECIPATVRSSFANQGEICLCTSRIFVQRSIYSEFLKRFVEATRKWKVGVPSDPSA 324
           DA+++  +   +   + N G+ C+C +R++VQ  +Y EF ++   A ++ KVG   D   
Sbjct: 268 DADIDAAVEGAMACKYRNSGQTCVCANRMYVQAGVYDEFCRKLTAAVQELKVGNGFDDGV 327

Query: 325 NMGALISKAHLEKVRSYVLKAQTEGARILCGEGVDQLSLPLRNQAG-YFMLPTVITDIKD 383
             G LI  A +E V S++  A  +G ++L G          R+  G  F  PT+I D+ D
Sbjct: 328 QQGPLIDMAAVETVESHIKDAVDKGGKVLAG--------GTRHALGRTFFAPTIIADVTD 379

Query: 384 ESRCMTEEIFGPVTCVVPFDSEEEVITRANSVRYGLAATVWSKDVGRIHRVAKKLQSGLV 443
           + R   EE FGP+  V  FD+EEEV+ +AN   +GLAA  +++D+ R  R+ +KL+ GLV
Sbjct: 380 DMRVAREETFGPLAPVFKFDTEEEVVRKANDTEFGLAAYFYTRDMARSWRIGEKLEYGLV 439

Query: 444 WTNCWLIRELNLPFGGMKSSGIGREGAKDSYDFFTEIK 481
             N  +I     PFGG+K SG GREG+K   D + EIK
Sbjct: 440 GINSGIISNPVAPFGGVKESGNGREGSKYGLDDYLEIK 477


Lambda     K      H
   0.319    0.134    0.404 

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: 529
Number of extensions: 23
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: 487
Length of database: 484
Length adjustment: 34
Effective length of query: 453
Effective length of database: 450
Effective search space:   203850
Effective search space used:   203850
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 (21.8 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