GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PRO3 in Methanospirillum lacunae Ki8-1

Align Pyrroline-5-carboxylate reductase 3; P5C reductase 3; P5CR 3; PCA reductase 3; EC 1.5.1.2 (characterized)
to candidate WP_109966884.1 DK846_RS00065 NAD(P)-binding domain-containing protein

Query= SwissProt::Q00777
         (272 letters)



>NCBI__GCF_003173355.1:WP_109966884.1
          Length = 272

 Score =  156 bits (394), Expect = 5e-43
 Identities = 91/271 (33%), Positives = 147/271 (54%), Gaps = 3/271 (1%)

Query: 1   MEQIGLIGYGSMADMIARQLLKHEQIKENELFIETRTKGERLRALMSDYPNVS-ADPLEN 59
           M+ IG IGYG M  M+    L+   +   ++ I TRT+ E++  L+  YP +  A     
Sbjct: 1   MKSIGFIGYGQMNCMLVEGFLQTSALNPEDIIISTRTR-EKVNPLLERYPEIRIATCNSE 59

Query: 60  WANTCQLILICVPPLHVIETMRRLYPYVNRNTHIVSIAAGVPLRLLEAETEAGISRVIPA 119
            A    LI+I V PL V   ++ +    +   HI+S+AA V   LL       I+R++P+
Sbjct: 60  VAEVADLIIIGVKPLEVTGILKEISGVRDNEIHIISLAACVSTDLLAQIHPGKITRILPS 119

Query: 120 ITSEAEAGISLVVHSEALAAEKKERLNELLSVFSRVREIKESNLDVASNLTSSAPGFIAA 179
           + S    GISL  H   +  +    + EL +  S V+ +KE   + A ++ S AP F++ 
Sbjct: 120 VCSTVGEGISLCYHHHRVTPDCARYVEELFTAISTVKLVKEELFEPAGDMMSCAPAFLSR 179

Query: 180 IFEELALSAVRNSSLSKEEAFDFLIHSLYGTGKMLIEKNMSFEETLERVATKGGITGEGA 239
            F E AL+  R+S+L+  E  + ++ + +GT  ML ++ M  E+ + RVAT GGIT EG 
Sbjct: 180 FFLEFALAGSRHSTLTLNECLEMVVSTAFGTALML-QEGMEPEDLIRRVATPGGITEEGV 238

Query: 240 EVIHASVPDVFDEVFERTLRKYELLTEQVGK 270
           +++   +P VFD +FE TL KY+L+  +V +
Sbjct: 239 KILERDLPAVFDRLFETTLSKYDLVKTRVSE 269


Lambda     K      H
   0.316    0.132    0.359 

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: 161
Number of extensions: 9
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: 272
Length of database: 272
Length adjustment: 25
Effective length of query: 247
Effective length of database: 247
Effective search space:    61009
Effective search space used:    61009
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 (21.6 bits)
S2: 47 (22.7 bits)

This GapMind analysis is from Sep 24 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