GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gabD in Desulfovibrio vulgaris Miyazaki F

Align NAD-dependent succinate semialdehyde dehydrogenase (EC 1.2.1.24) (characterized)
to candidate 8502217 DvMF_2927 tartronate semialdehyde reductase (RefSeq)

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



>FitnessBrowser__Miya:8502217
          Length = 299

 Score =  148 bits (374), Expect = 1e-40
 Identities = 88/287 (30%), Positives = 137/287 (47%)

Query: 1   MEEIGFLGIGIMGKAMAVNLLRHGFKVTVWNRTLSRCDELVQHGASVGETPAEVIKKCKY 60
           M+ IGF+G+GIMG  M  NLL+ GF VT + R   +   +   GA+  E+PA V      
Sbjct: 1   MQRIGFIGLGIMGAPMCRNLLKAGFPVTAYTRNGDKLRAMAAEGAAAAESPAAVAAASDV 60

Query: 61  TIAMLSDPAAALSVVFDKHGALEHICAGKGYIDMSTVDADTSSQISQAITSKGGSFLEAP 120
            I ML +     +V     G  E    G    DMS++    S +I+  +  K    L+AP
Sbjct: 61  VITMLPNSPEVRAVALGPGGIAEGAAPGCIVADMSSIAPLASREIAAELAKKSIRMLDAP 120

Query: 121 VSGSKKPAEDGQLVILAAGDKDLYDQVVPAFDVLGKKSFFLGKIGNGAKMKLVVNMIMGS 180
           VSG +  A DG L ++  G ++ +D  +P F  +      +G++G G   KL   +++  
Sbjct: 121 VSGGEPKAIDGTLSVMVGGAQEDFDACLPVFKAMAASVVRVGEVGAGNVTKLANQIVVAG 180

Query: 181 MMNAFSEGIVLADKSGLDPHTLLDVLDLGAIANPMFKMKGPAMIKNSYPPAFPLKHQQKD 240
            + A SE +VLA ++G DP  +   +  G   + +   K P ++   + P F ++   KD
Sbjct: 181 NIAAMSEALVLATRAGADPDLVYQAIRGGLAGSTVLDAKAPLVMDGRFTPGFRIRLHAKD 240

Query: 241 MRLALALGDENAVPMPVAAAANEAFKKARSLGLGDLDFSAVFETLSK 287
           M   L    E  VP+P+AA   E  +   + GLGD D  A+     K
Sbjct: 241 MGNVLETSRELHVPLPLAAQLMEVMQGLMADGLGDADHGALIRHWEK 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: 187
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: 299
Length adjustment: 26
Effective length of query: 261
Effective length of database: 273
Effective search space:    71253
Effective search space used:    71253
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: 48 (23.1 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:

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