GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gabD in Geotalea uraniireducens Rf4

Align NAD-dependent succinate semialdehyde dehydrogenase (EC 1.2.1.24) (characterized)
to candidate WP_011937525.1 GURA_RS02990 NAD(P)-dependent oxidoreductase

Query= metacyc::MONOMER-15565
         (287 letters)



>NCBI__GCF_000016745.1:WP_011937525.1
          Length = 287

 Score =  345 bits (884), Expect = e-100
 Identities = 170/287 (59%), Positives = 215/287 (74%)

Query: 1   MEEIGFLGIGIMGKAMAVNLLRHGFKVTVWNRTLSRCDELVQHGASVGETPAEVIKKCKY 60
           M + GFLG+GIMG AMA NLL+ GF VTVWNR+  +C+EL   GA    TP +V++ C  
Sbjct: 1   MNKFGFLGLGIMGSAMAKNLLKAGFDVTVWNRSPEKCEELAALGARSAATPRQVVESCGI 60

Query: 61  TIAMLSDPAAALSVVFDKHGALEHICAGKGYIDMSTVDADTSSQISQAITSKGGSFLEAP 120
           T AMLSDPAA  +V F   G LE I AGKGY+DMSTVDA T+ +I  A+T KGG FLEAP
Sbjct: 61  TFAMLSDPAADEAVCFGTDGVLEGIGAGKGYVDMSTVDATTAQKIGAAVTDKGGRFLEAP 120

Query: 121 VSGSKKPAEDGQLVILAAGDKDLYDQVVPAFDVLGKKSFFLGKIGNGAKMKLVVNMIMGS 180
           VSGS+KPAEDG L+IL AGDK LY++ +PAF+ +GKK  FLG++G GA+MKLVVNM+MG 
Sbjct: 121 VSGSRKPAEDGTLIILTAGDKSLYNEAMPAFERMGKKVLFLGEVGKGAEMKLVVNMVMGG 180

Query: 181 MMNAFSEGIVLADKSGLDPHTLLDVLDLGAIANPMFKMKGPAMIKNSYPPAFPLKHQQKD 240
           MM+ F EG+ L  K+GL+   +LDV+D GA+ANPMFK+KG  +   ++  AFPLKH QKD
Sbjct: 181 MMSIFCEGLALGAKAGLEVTDMLDVMDAGAVANPMFKLKGGLIAAGNFTTAFPLKHMQKD 240

Query: 241 MRLALALGDENAVPMPVAAAANEAFKKARSLGLGDLDFSAVFETLSK 287
           +RLA+ LGD    P+  AAAANEAFK+A++LG GD DFSA+F+ + K
Sbjct: 241 LRLAVGLGDWLGQPLFTAAAANEAFKRAKALGFGDEDFSALFKAIEK 287


Lambda     K      H
   0.318    0.135    0.384 

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: 290
Number of extensions: 4
Number of successful extensions: 1
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: 287
Length of database: 287
Length adjustment: 26
Effective length of query: 261
Effective length of database: 261
Effective search space:    68121
Effective search space used:    68121
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: 47 (22.7 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