GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dpkA in Rhodobacter viridis JA737

Align 1-piperideine-2-carboxylate/1-pyrroline-2-carboxylate reductase [NAD(P)H] (EC 1.5.1.1) (characterized)
to candidate WP_110804622.1 C8J30_RS05020 ornithine cyclodeaminase

Query= BRENDA::Q485R8
         (316 letters)



>NCBI__GCF_003217355.1:WP_110804622.1
          Length = 304

 Score =  125 bits (315), Expect = 1e-33
 Identities = 79/249 (31%), Positives = 130/249 (52%), Gaps = 9/249 (3%)

Query: 65  KAFTYFPDNAKKHDLPGLFSKIMLFKRQTGEPLALVDGTSVTYWRTAAISALASQLLSRK 124
           KA T  P NA   DLP +   +ML + +TG   A++D   VT W+TA  S LA++LL+R 
Sbjct: 61  KAATIVPGNAGV-DLPTVNGGVMLMEDRTGLLSAVLDFALVTKWKTAGDSLLAARLLARP 119

Query: 125 NSQHLMLFGTGNLASYLVKAHLTVRDIKQVTLWGRNAKKVSKLIADFSILYPAVTFKTSV 184
            +  +++ G G +A+ +++A+       + T+W R+        A    L  A   +  +
Sbjct: 120 EATEILICGAGKVAAAMIEAYRAAFPAARFTIWNRSQ-------AGAEALAEATGARVEM 172

Query: 185 DVNAEVASADIICCATGAKTPLFDGNSVSAGCHIDCLGNHMTDARECDTTTILRARVFVD 244
           ++   +  A+I+   T AK P   G+ +  G HID +G    D RE D  T+ RAR+F D
Sbjct: 173 NLETALGQAEIVAGTTMAKDPWLRGDWLQPGTHIDLIGAFRPDMREADDATLRRARLFCD 232

Query: 245 SLTNTLNEAGELLIPMAEDAFNKDEIVGELADMCKTPSMLRQSSDEITLFKSVGTAISDL 304
           +   TL+  GE   P++     + ++V +  D+  T    R+S+DEITL K+ G A  DL
Sbjct: 233 ARATTLHHIGEFRDPLSRGVIAETDVVADFYDIA-TGRFARESADEITLSKNGGGAHLDL 291

Query: 305 VAAHSVVEK 313
           + A  + ++
Sbjct: 292 MTASFIRDR 300


Lambda     K      H
   0.318    0.131    0.379 

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: 183
Number of extensions: 8
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: 316
Length of database: 304
Length adjustment: 27
Effective length of query: 289
Effective length of database: 277
Effective search space:    80053
Effective search space used:    80053
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: 48 (23.1 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