Alignments for a candidate for argI in Chlorobaculum tepidum TLS

GapMind for Amino acid biosynthesis

Alignments for a candidate for argI in Chlorobaculum tepidum TLS

Align ornithine carbamoyltransferase (EC 2.1.3.3) (characterized)
to candidate NP_662003.1 CT1112 ornithine carbamoyltransferase

Query= BRENDA::O93656
         (317 letters)



>NCBI__GCF_000006985.1:NP_662003.1
          Length = 338

 Score =  292 bits (747), Expect = 9e-84
 Identities = 145/269 (53%), Positives = 192/269 (71%), Gaps = 3/269 (1%)

Query: 42  RLLEGKTLAMIFQKPSTRTRVSFEVAMAHLGGHALYLNAQDLQLRRGETIADTARVLSRY 101
           R +  KT+AMIF KPS RTRVSFE+ +  LGGHA+ L  + + +   E+I D AR+LSRY
Sbjct: 50  RPIRHKTVAMIFNKPSLRTRVSFELGVYELGGHAISLEGKSIGVGERESIEDIARLLSRY 109

Query: 102 VDAIMARVYDHKDVEDLAKYASVPVINGLSDFSHPCQALADYMTIWEKKGTIKGVKVVYV 161
            DAI+AR+++H+ +E LAK+A +PVIN L+D SHPCQ LAD  T++EK      +KVV+V
Sbjct: 110 NDAIVARLHEHEIIETLAKHADIPVINALTDLSHPCQVLADAFTLYEKGLWRDDIKVVFV 169

Query: 162 GDGNNVAHSLMIAGTKLGADVVVATPEGYEPDEKVIKWAEQNAAESGGSFELLHDPVKAV 221
           GDGNNVA+S +     L    V+A PEGY PDE ++K A  NA    G+ E+LHDP++A 
Sbjct: 170 GDGNNVANSWIELAGILPFHFVLACPEGYLPDETLLKQARSNAK---GTIEILHDPMEAA 226

Query: 222 KDADVIYTDVWASMGQEAEAEERRKIFRPFQVNKDLVKHAKPDYMFMHCLPAHRGEEVTD 281
           K ADV+YTDVW SMGQE E  ER K F PFQ+N  +V  AKP  + MHC+PAHRG+E++ 
Sbjct: 227 KQADVLYTDVWTSMGQEEEMAERLKAFAPFQINAKMVAEAKPSAVIMHCMPAHRGQEISA 286

Query: 282 DVIDSPNSVVWDEAENRLHAQKAVLALLL 310
           +V+D P S++ DEAENRLH QKA++  L+
Sbjct: 287 EVMDGPQSIIIDEAENRLHVQKALMVKLM 315


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: 293
Number of extensions: 12
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: 317
Length of database: 338
Length adjustment: 28
Effective length of query: 289
Effective length of database: 310
Effective search space:    89590
Effective search space used:    89590
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 (21.7 bits)
S2: 48 (23.1 bits)

Align candidate NP_662003.1 CT1112 (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.30527.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                              -----------
   5.4e-113  363.1   0.0   6.2e-113  362.9   0.0    1.0  1  lcl|NCBI__GCF_000006985.1:NP_662003.1  CT1112 ornithine carbamoyltransf


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000006985.1:NP_662003.1  CT1112 ornithine carbamoyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  362.9   0.0  6.2e-113  6.2e-113       1     303 [.      13     315 ..      13     316 .. 0.96

  Alignments for each domain:
  == domain 1  score: 362.9 bits;  conditional E-value: 6.2e-113
                              TIGR00658   1 rhllslldlseeelkellelakklkkekkkgke...ekklkgktlaliFekrstRtRvsfevaayelGaqvl 69 
                                            r++l ++ l+ +++ el +++  +k++++++++    + ++ kt+a+iF+k+s RtRvsfe ++yelG++++
  lcl|NCBI__GCF_000006985.1:NP_662003.1  13 RDFLGFTGLDAAKIIELFDYSLFIKQQRETNRNsdeFRPIRHKTVAMIFNKPSLRTRVSFELGVYELGGHAI 84 
                                            6899999999***************99999887322456789****************************** PP

                              TIGR00658  70 ylnkeelqlgrkesikDtarvlsryvdaivvRvykhedveelakyasvPvingLtdlehPcqilaDlltike 141
                                             l+ +++ +g++esi+D ar lsry daiv+R ++he++e+lak+a +Pvin+Ltdl+hPcq+laD +t++e
  lcl|NCBI__GCF_000006985.1:NP_662003.1  85 SLEGKSIGVGERESIEDIARLLSRYNDAIVARLHEHEIIETLAKHADIPVINALTDLSHPCQVLADAFTLYE 156
                                            ************************************************************************ PP

                              TIGR00658 142 klgklkevklvyvGDannvanslllaaaklGldvvvatPeglepeaeivkkakkiakenggkleltedpkka 213
                                            k    +++k+v+vGD+nnvans +  a  l +++v+a+Peg+ p+++++k+a+    +  g++e+++dp +a
  lcl|NCBI__GCF_000006985.1:NP_662003.1 157 KGLWRDDIKVVFVGDGNNVANSWIELAGILPFHFVLACPEGYLPDETLLKQARS---NAKGTIEILHDPMEA 225
                                            *999************************************************87...56699********** PP

                              TIGR00658 214 vkdadviytDvwvsmGeeekkeerlkllkpyqvneellelakpevkflhCLPavrGeevtdevlegeasivf 285
                                            +k+adv+ytDvw+smG+ee+ +erlk++ p+q+n ++++ akp+++++hC+Pa+rG+e++ ev++g++si+ 
  lcl|NCBI__GCF_000006985.1:NP_662003.1 226 AKQADVLYTDVWTSMGQEEEMAERLKAFAPFQINAKMVAEAKPSAVIMHCMPAHRGQEISAEVMDGPQSIII 297
                                            ************************************************************************ PP

                              TIGR00658 286 deaenRlhaqkavlkall 303
                                            deaenRlh+qka+++ l+
  lcl|NCBI__GCF_000006985.1:NP_662003.1 298 DEAENRLHVQKALMVKLM 315
                                            **************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (304 nodes)
Target sequences:                          1  (338 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 7.12
//
[ok]

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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