GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rocA in Sinorhizobium fredii NGR234

Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate WP_015886765.1 NGR_RS03130 aldehyde dehydrogenase family protein

Query= BRENDA::P30038
         (563 letters)



>NCBI__GCF_000018545.1:WP_015886765.1
          Length = 475

 Score =  115 bits (289), Expect = 3e-30
 Identities = 102/337 (30%), Positives = 151/337 (44%), Gaps = 23/337 (6%)

Query: 202 GFVAAISPFNF--TAIGGNLAGAPALMGNVVLWKPSDTAMLASYAVYRILREAGLPPNII 259
           G VA I+P+N+    I   +A A A    +VL KPS+ A   +     I+ EAG+P  + 
Sbjct: 138 GVVAMITPWNWPINQIACKVAAALATGCTMVL-KPSEIAPFNAVLFAEIMDEAGVPKGVF 196

Query: 260 QFVPADGPLFGDTVTSSEHLCGINFTGSVPTFKHLWKQVAQNLDRFHTFPRLAGECGGKN 319
             V  DGP  G  + S   +  ++FTGS      + +  A  + R H       E GGK+
Sbjct: 197 NLVQGDGPTVGAALASHPDVDMVSFTGSTRAGIAVAQAAAPTVKRVHQ------ELGGKS 250

Query: 320 FHFVHRSADVESVVSGTLRSAFEYGGQKCSACSRLYVPHSLWPQIKGRLLEEHSRIKVGD 379
            + + RSAD  + V+  +R  F   GQ C+A +R+ VP     +       +   + VG 
Sbjct: 251 PNIILRSADFPAAVAAGVRRCFGNSGQTCTAPTRMLVPAERMDEAGAIAARQADALVVGP 310

Query: 380 PAEDFGTFFSAVIDAKSFARIKKWLEHARSSPSLTILAGGKCDDS---VGYFVEPCIVES 436
           P+ D  T    V  A  F +I+  +E    +    ++AGG    S    GY+V P +   
Sbjct: 311 PS-DSRTDLGPVASAAQFDKIQALIERG-IAEGAELVAGGLGRPSHLNAGYYVRPTVFAR 368

Query: 437 KDPQEPIMKEEIFGPVLSVYVYPDDKYKETLQLVDSTTSYGLTGAVFSQDKDVVQEATKV 496
              Q  I +EEIFGPVLS+  Y  D   E +  V + T YGL   +    K+    A K+
Sbjct: 369 VTNQMSIAREEIFGPVLSIIGY--DSEDEAI-AVANDTPYGLAAYIQGDPKETRALAGKL 425

Query: 497 LRNAAGNFYINDKSTGSIVGQQPFGGARASGTNDKPG 533
               +G   +N     S     PFGG + SG   + G
Sbjct: 426 ---RSGTVRLNSSGWDSAA---PFGGYKQSGNGREYG 456


Lambda     K      H
   0.319    0.135    0.411 

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: 569
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: 563
Length of database: 475
Length adjustment: 35
Effective length of query: 528
Effective length of database: 440
Effective search space:   232320
Effective search space used:   232320
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 Apr 09 2024. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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