GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ocd in Hydrogenophaga taeniospiralis CCUG 15921 NBRC 102512

Align Ornithine cyclodeaminase; OCD; EC 4.3.1.12 (characterized)
to candidate WP_068166973.1 HTA01S_RS02545 ornithine cyclodeaminase family protein

Query= SwissProt::P09773
         (354 letters)



>NCBI__GCF_001592305.1:WP_068166973.1
          Length = 329

 Score =  105 bits (262), Expect = 2e-27
 Identities = 84/264 (31%), Positives = 123/264 (46%), Gaps = 27/264 (10%)

Query: 56  SHSRDGVIELMPTSDGTLYGFKYVNGHPKNTKSGRQTVTAFGVLSDVDSGYPLLLSEMTI 115
           SHS    I  M  S G        +G P    SG  TV  F    D  S   + + + ++
Sbjct: 57  SHSAANEIISMKASSGGFPNNPIDHGVP----SGMGTVLLF----DARSCALICVMDGSL 108

Query: 116 LTALRTAATSAIAAKYLARKDSRTMALIGNGAQSEFQALAFKALIGVDRIRLYDIDPEAT 175
           LT LRT A  A++ K LARK+ +T+  IG G Q+  Q  A   ++ ++ I  +D  PE  
Sbjct: 109 LTGLRTGAAGAVSVKALARKNVKTVTSIGTGKQARMQIRAIHHVMKIEEIHAWDHHPENL 168

Query: 176 ARCSRNLQ-RFGFQIEACTSAEQAVEGADIITTATADKHNATILSDNMIGPGVHINGVGG 234
           AR   +++  FG  +    S + AVE A I+ T T  K    ++    I PG HI  +G 
Sbjct: 169 ARYKADIEGEFGIPVVMARSMQAAVEQAHILITTTRGK--GALVEAAWIQPGTHIVAMGT 226

Query: 235 DCPGKTEMHRDILLRSDIFVEFPPQTRIEGEIQQLAPDHPV-----------TELWRVMT 283
           D  GK E   +I   + I  +   Q   +GE       HP+            EL  ++ 
Sbjct: 227 DTYGKQEFEPEIFRGAKIVNDSIAQCIEKGETW-----HPLNRNIIRREDIHAELGEILL 281

Query: 284 GQDVGRKSDKQITLFDSVGFAIED 307
           G+  GR++D +IT+FDS G AI+D
Sbjct: 282 GKKPGRETDHEITIFDSTGMAIQD 305


Lambda     K      H
   0.320    0.137    0.396 

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: 229
Number of extensions: 11
Number of successful extensions: 4
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: 354
Length of database: 329
Length adjustment: 29
Effective length of query: 325
Effective length of database: 300
Effective search space:    97500
Effective search space used:    97500
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 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