Alignments for a candidate for argI in Synechococcus elongatus PCC 7942

GapMind for Amino acid biosynthesis

Alignments for a candidate for argI in Synechococcus elongatus PCC 7942

Align ornithine carbamoyltransferase (EC 2.1.3.3) (characterized)
to candidate Synpcc7942_2514 Synpcc7942_2514 ornithine carbamoyltransferase

Query= BRENDA::Q51742
         (315 letters)



>FitnessBrowser__SynE:Synpcc7942_2514
          Length = 305

 Score =  303 bits (775), Expect = 4e-87
 Identities = 160/312 (51%), Positives = 211/312 (67%), Gaps = 8/312 (2%)

Query: 3   VSLAGRDLLCLQDYTAEEIWTILETAKMFKIWQK-IGKPHRLLEGKTLAMIFQKPSTRTR 61
           + LAGRDLL L D ++ E+  ILE A   K  Q  +  P      KTL +IF K STRTR
Sbjct: 1   MGLAGRDLLTLADLSSAEVLEILELAATLKSGQTTVHCP------KTLGLIFSKSSTRTR 54

Query: 62  VSFEVAMAHLGGHALYLNAQDLQLRRGETIADTARVLSRYVDAIMARVYDHKDVEDLAKY 121
           VSF  A+  +GG  L LN    Q+ RGE IADTARVLSRY+DA+  R +  +D+E+ A Y
Sbjct: 55  VSFSAAIMQMGGQVLDLNPNVTQVGRGEPIADTARVLSRYLDALAIRTFAQQDLEEYAHY 114

Query: 122 ATVPVINGLSDFSHPCQALADYMTIWEKKGTIKGVKVVYVGDGNNVAHSLMIAGTKLGAD 181
           A +PVIN L+D  HPCQ LAD  TI E  G  + + + Y+GDGNNVAHSL++   ++G +
Sbjct: 115 ADIPVINALTDDYHPCQILADLQTIQENFGQWQDLTLTYLGDGNNVAHSLLLGCAQVGMN 174

Query: 182 VVVATPEGYEPDEKVIKWAEQNAAESGGSFELLHDPVKAVKDADVIYTDVWASMGQEAEA 241
           V +A P  Y+P E+++  A+Q A +     E+LHDP+ A + A V+YTDVWASMGQE EA
Sbjct: 175 VRIACPPDYQPQERIVAKAQQIAGDR-AKVEILHDPIAASQGAHVLYTDVWASMGQEEEA 233

Query: 242 EERRKIFRPFQVNKDLVKHAKPDYMFMHCLPAHRGEEVTDDVIDSPNSVVWDQAENRLHA 301
           + R K F P+Q+N+ L++ A P  + +HCLPAHR EE+T +V++   S VWDQAENRLHA
Sbjct: 234 QARVKAFTPYQLNQALLEKADPAAIVLHCLPAHREEEITAEVLEGSQSRVWDQAENRLHA 293

Query: 302 QKAVLALVMGGI 313
           QKAVLAL++G I
Sbjct: 294 QKAVLALLLGAI 305


Lambda     K      H
   0.319    0.134    0.400 

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: 283
Number of extensions: 14
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: 315
Length of database: 305
Length adjustment: 27
Effective length of query: 288
Effective length of database: 278
Effective search space:    80064
Effective search space used:    80064
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)

Align candidate Synpcc7942_2514 Synpcc7942_2514 (ornithine carbamoyltransferase)
to HMM TIGR00658 (argF: ornithine carbamoyltransferase (EC 2.1.3.3))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.aa/TIGR00658.hmm
# target sequence database:        /tmp/gapView.22428.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00658  [M=304]
Accession:   TIGR00658
Description: orni_carb_tr: ornithine carbamoyltransferase
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                                 Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   6.3e-129  415.5   0.0   7.1e-129  415.3   0.0    1.0  1  lcl|FitnessBrowser__SynE:Synpcc7942_2514  Synpcc7942_2514 ornithine carbam


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__SynE:Synpcc7942_2514  Synpcc7942_2514 ornithine carbamoyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  415.3   0.0  7.1e-129  7.1e-129       1     303 [.       6     302 ..       6     303 .. 0.98

  Alignments for each domain:
  == domain 1  score: 415.3 bits;  conditional E-value: 7.1e-129
                                 TIGR00658   1 rhllslldlseeelkellelakklkkekkkgkeekklkgktlaliFekrstRtRvsfevaayelGaqvl 69 
                                               r+ll+l+dls++e+ e+lela++lk+ +++       + ktl+liF k+stRtRvsf +a++++G+qvl
  lcl|FitnessBrowser__SynE:Synpcc7942_2514   6 RDLLTLADLSSAEVLEILELAATLKSGQTT-----VHCPKTLGLIFSKSSTRTRVSFSAAIMQMGGQVL 69 
                                               79************************9988.....3489****************************** PP

                                 TIGR00658  70 ylnkeelqlgrkesikDtarvlsryvdaivvRvykhedveelakyasvPvingLtdlehPcqilaDllt 138
                                                ln++ +q+gr+e+i+Dtarvlsry+da+++R+++++d+ee a+ya +Pvin+Ltd  hPcqilaDl+t
  lcl|FitnessBrowser__SynE:Synpcc7942_2514  70 DLNPNVTQVGRGEPIADTARVLSRYLDALAIRTFAQQDLEEYAHYADIPVINALTDDYHPCQILADLQT 138
                                               ********************************************************************* PP

                                 TIGR00658 139 ikeklgklkevklvyvGDannvanslllaaaklGldvvvatPeglepeaeivkkakkiakenggklelt 207
                                               i+e++g+ ++++l+y+GD+nnva+slll++a++G++v++a+P++++p+++iv ka++ia    +k+e++
  lcl|FitnessBrowser__SynE:Synpcc7942_2514 139 IQENFGQWQDLTLTYLGDGNNVAHSLLLGCAQVGMNVRIACPPDYQPQERIVAKAQQIAG-DRAKVEIL 206
                                               *******************************************************99765.569***** PP

                                 TIGR00658 208 edpkkavkdadviytDvwvsmGeeekkeerlkllkpyqvneellelakpevkflhCLPavrGeevtdev 276
                                               +dp  a+++a+v+ytDvw+smG+ee++++r+k++ pyq+n+ lle a+p +++lhCLPa+r ee+t ev
  lcl|FitnessBrowser__SynE:Synpcc7942_2514 207 HDPIAASQGAHVLYTDVWASMGQEEEAQARVKAFTPYQLNQALLEKADPAAIVLHCLPAHREEEITAEV 275
                                               ********************************************************************* PP

                                 TIGR00658 277 legeasivfdeaenRlhaqkavlkall 303
                                               leg++s+v+d+aenRlhaqkavl++ll
  lcl|FitnessBrowser__SynE:Synpcc7942_2514 276 LEGSQSRVWDQAENRLHAQKAVLALLL 302
                                               ***********************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (304 nodes)
Target sequences:                          1  (305 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 10.43
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer
changes to Amino acid biosynthesis since the publication.

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

GapMind for Amino acid biosynthesis