Alignments for a candidate for argI in Thioalkalivibrio paradoxus ARh 1

GapMind for Amino acid biosynthesis

Alignments for a candidate for argI in Thioalkalivibrio paradoxus ARh 1

Align Ornithine carbamoyltransferase, anabolic; OTCase; EC 2.1.3.3 (characterized)
to candidate WP_006748313.1 THITH_RS09655 ornithine carbamoyltransferase

Query= SwissProt::P11724
         (305 letters)



>NCBI__GCF_000227685.2:WP_006748313.1
          Length = 303

 Score =  361 bits (927), Expect = e-104
 Identities = 181/300 (60%), Positives = 223/300 (74%), Gaps = 1/300 (0%)

Query: 1   MSVRHFLSFMDYSPEELIGLIRRGSELKDLRNRGVLYEPL-KSRVLGMVFEKASTRTRLS 59
           M++RHFLSF D S  E+  +I+R  ELK     GV ++ L + + LGM+FEK+STRTR+S
Sbjct: 1   MTLRHFLSFSDLSGSEVRTIIQRAIELKRQTRAGVAHDYLLRGKTLGMIFEKSSTRTRVS 60

Query: 60  FEAGMIQLGGQAIFLSPRDTQLGRGEPIGDSARVMSRMLDGVMIRTFAHATLTEFAAHSK 119
           FE GM+QLGG A+FLSPRDTQLGRGEPI D+ARV+SRM+D VMIRT+ H  +  FA H+ 
Sbjct: 61  FEVGMLQLGGHALFLSPRDTQLGRGEPIEDTARVLSRMVDAVMIRTYEHEKIERFAQHAT 120

Query: 120 VPVINGLSDDLHPCQLLADMQTFHEHRGSIQGKTVAWIGDGNNMCNSYIEAALKFDFQLR 179
           VPVINGL+D  HP QLLAD+QT+ E RG I G+ VAWIGDGNNMCNSYI AA +  F L 
Sbjct: 121 VPVINGLTDHEHPAQLLADLQTYTEQRGDIGGRRVAWIGDGNNMCNSYILAARQLGFTLA 180

Query: 180 VACPEGYEPKAEFVALAGDRLRVVRDPREAVAGAHLVSTDVWASMGQEDEAAARIALFRP 239
            ACPEGY+P    V  AGD L ++RDP  A   A LV TDVWASMGQEDE +AR   F  
Sbjct: 181 AACPEGYDPDPGIVKAAGDALELLRDPAAATRDADLVVTDVWASMGQEDEKSARRQAFTG 240

Query: 240 YQVNAALLDGAADDVLFMHCLPAHRGEEISEELLDDPRSVAWDQAENRLHAQKALLELLI 299
           + V++ L+  A  D LFMHCLPAHR EE++ E+L+ P+SV W++AENRLHAQKAL+E L+
Sbjct: 241 FLVDSELMALARPDALFMHCLPAHREEEVTTEVLEGPQSVVWEEAENRLHAQKALVEFLL 300


Lambda     K      H
   0.322    0.136    0.404 

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: 301
Number of extensions: 7
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: 305
Length of database: 303
Length adjustment: 27
Effective length of query: 278
Effective length of database: 276
Effective search space:    76728
Effective search space used:    76728
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 (21.9 bits)
S2: 48 (23.1 bits)

Align candidate WP_006748313.1 THITH_RS09655 (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.29041.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.1e-124  400.6   0.0   2.3e-124  400.4   0.0    1.0  1  lcl|NCBI__GCF_000227685.2:WP_006748313.1  THITH_RS09655 ornithine carbamoy


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000227685.2:WP_006748313.1  THITH_RS09655 ornithine carbamoyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  400.4   0.0  2.3e-124  2.3e-124       1     303 [.       4     300 ..       4     301 .. 0.98

  Alignments for each domain:
  == domain 1  score: 400.4 bits;  conditional E-value: 2.3e-124
                                 TIGR00658   1 rhllslldlseeelkellelakklkkekkkgkeekk.lkgktlaliFekrstRtRvsfevaayelGaqv 68 
                                               rh+ls+ dls +e+++++++a +lk+++++g+ +++ l+gktl++iFek+stRtRvsfev++ +lG+++
  lcl|NCBI__GCF_000227685.2:WP_006748313.1   4 RHFLSFSDLSGSEVRTIIQRAIELKRQTRAGVAHDYlLRGKTLGMIFEKSSTRTRVSFEVGMLQLGGHA 72 
                                               8******************************99876268****************************** PP

                                 TIGR00658  69 lylnkeelqlgrkesikDtarvlsryvdaivvRvykhedveelakyasvPvingLtdlehPcqilaDll 137
                                               l+l++ ++qlgr+e+i+Dtarvlsr+vda+++R+y+he++e +a++a+vPvingLtd+ehP q+laDl+
  lcl|NCBI__GCF_000227685.2:WP_006748313.1  73 LFLSPRDTQLGRGEPIEDTARVLSRMVDAVMIRTYEHEKIERFAQHATVPVINGLTDHEHPAQLLADLQ 141
                                               ********************************************************************* PP

                                 TIGR00658 138 tikeklgklkevklvyvGDannvanslllaaaklGldvvvatPeglepeaeivkkakkiakenggklel 206
                                               t +e+ g++ + +++++GD+nn++ns +laa +lG+++  a+Peg++p++ ivk a       g  lel
  lcl|NCBI__GCF_000227685.2:WP_006748313.1 142 TYTEQRGDIGGRRVAWIGDGNNMCNSYILAARQLGFTLAAACPEGYDPDPGIVKAA-------GDALEL 203
                                               *****************************************************998.......789*** PP

                                 TIGR00658 207 tedpkkavkdadviytDvwvsmGeeekkeerlkllkpyqvneellelakpevkflhCLPavrGeevtde 275
                                               ++dp+ a++dad+++tDvw+smG+e++k++r +++ ++ v++el++la p++ f+hCLPa+r eevt e
  lcl|NCBI__GCF_000227685.2:WP_006748313.1 204 LRDPAAATRDADLVVTDVWASMGQEDEKSARRQAFTGFLVDSELMALARPDALFMHCLPAHREEEVTTE 272
                                               ********************************************************************* PP

                                 TIGR00658 276 vlegeasivfdeaenRlhaqkavlkall 303
                                               vleg++s+v++eaenRlhaqka++++ll
  lcl|NCBI__GCF_000227685.2:WP_006748313.1 273 VLEGPQSVVWEEAENRLHAQKALVEFLL 300
                                               ************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (304 nodes)
Target sequences:                          1  (303 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: 6.70
//
[ok]

This GapMind analysis is from Apr 10 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