GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argF'B in Synechococcus elongatus PCC 7942

Align N-succinylornithine carbamoyltransferase; EC 2.1.3.11 (characterized, see rationale)
to candidate Synpcc7942_2514 Synpcc7942_2514 ornithine carbamoyltransferase

Query= uniprot:L0G4Z0_ECHVK
         (313 letters)



>FitnessBrowser__SynE:Synpcc7942_2514
          Length = 305

 Score =  104 bits (260), Expect = 2e-27
 Identities = 87/290 (30%), Positives = 136/290 (46%), Gaps = 41/290 (14%)

Query: 37  KRIGLLFLNPSLRTRVSTQIAASNLGMESIVLNMDKESWALEMEDGVIMNQGKAEHIRDA 96
           K +GL+F   S RTRVS   A   +G + + LN +            +   G+ E I D 
Sbjct: 40  KTLGLIFSKSSTRTRVSFSAAIMQMGGQVLDLNPN------------VTQVGRGEPIADT 87

Query: 97  AGVLGSYFDILALRAFPSLTNKDEDSEDFILHQFAKHSGLPLISLESAIRHPLQSLADMV 156
           A VL  Y D LA+R F              L ++A ++ +P+I+  +   HP Q LAD+ 
Sbjct: 88  ARVLSRYLDALAIRTFAQQD----------LEEYAHYADIPVINALTDDYHPCQILADLQ 137

Query: 157 TIQEHKQKEKPKVVLTWAPHIKAIPHAVANSFAEWSIGCGHDVTITHPEGYELDERFTQG 216
           TIQE+  + +  + LT+      + H++    A+     G +V I  P  Y+  ER    
Sbjct: 138 TIQENFGQWQD-LTLTYLGDGNNVAHSLLLGCAQ----VGMNVRIACPPDYQPQERIVAK 192

Query: 217 AT----------IEHDQDKALANADFVYVKNWSAFNEYGKILCTDES---WMLNEQKLSQ 263
           A           I HD   A   A  +Y   W++  +  +     ++   + LN+  L +
Sbjct: 193 AQQIAGDRAKVEILHDPIAASQGAHVLYTDVWASMGQEEEAQARVKAFTPYQLNQALLEK 252

Query: 264 A-PNAKVMHCLPVRRNVELSDEILDGPRSLVQHQAKNRVFAAQAALSELL 312
           A P A V+HCLP  R  E++ E+L+G +S V  QA+NR+ A +A L+ LL
Sbjct: 253 ADPAAIVLHCLPAHREEEITAEVLEGSQSRVWDQAENRLHAQKAVLALLL 302


Lambda     K      H
   0.317    0.132    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: 182
Number of extensions: 8
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: 313
Length of database: 305
Length adjustment: 27
Effective length of query: 286
Effective length of database: 278
Effective search space:    79508
Effective search space used:    79508
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 Aug 03 2021. The underlying query database was built on Aug 03 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