GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ocd in Pseudomonas putida KT2440

Align Ornithine cyclodeaminase; OCD; EC 4.3.1.12 (characterized)
to candidate PP_4431 PP_4431 Ornithine cyclodeaminase 1

Query= SwissProt::Q59701
         (356 letters)



>FitnessBrowser__Putida:PP_4431
          Length = 330

 Score =  102 bits (255), Expect = 1e-26
 Identities = 67/207 (32%), Positives = 111/207 (53%), Gaps = 10/207 (4%)

Query: 109 LLSEMTILTALRTAATSALAAKYLARPNSKTMAIIGNGAQSEFQARAFRAILGIQKLRLF 168
           LL +   LTA+RTAA  A+AA++LAR +S+ +A++G G Q+E Q +A   +  I+++R++
Sbjct: 104 LLLDNGYLTAVRTAAAGAVAARWLARQDSEEVALLGAGEQAELQLKALLLVRDIKRVRVW 163

Query: 169 DIDTSATRKCARNLTGP-GFDIVECGSVAEAVEGADVITTVTADKQFATILSDNHVGPGV 227
              ++  ++ A  L+   G +     SV EA+  AD+  T T   Q   IL   H+ PG+
Sbjct: 164 ARSSAKAQQLALQLSSLYGLEATAAESVDEAMSSADIAVTCTPSNQ--PILHRRHLRPGL 221

Query: 228 HINAVGGDCPGKTEISMEVLLRSDIFV-EYPPQTWIEGDIQQLPRT------HPVTELWQ 280
           HI A+G D   K E++ EV+   D +V +   QT   G++                EL Q
Sbjct: 222 HITAMGADTEHKNEVAPEVIAAVDHYVADRVSQTATLGELHHAINAGVAQDLRVYAELGQ 281

Query: 281 VMTGEKTGRVGDRQITMFDSVGFAIED 307
           V+ G++ GR+    +T+ D  G  ++D
Sbjct: 282 VILGDRVGRLTPTDVTLCDLTGTGVQD 308


Lambda     K      H
   0.320    0.137    0.405 

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: 198
Number of extensions: 5
Number of successful extensions: 2
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: 356
Length of database: 330
Length adjustment: 29
Effective length of query: 327
Effective length of database: 301
Effective search space:    98427
Effective search space used:    98427
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: 49 (23.5 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