Alignments for a candidate for argI in Desulfotalea psychrophila LSv54

GapMind for Amino acid biosynthesis

Alignments for a candidate for argI in Desulfotalea psychrophila LSv54

Align Ornithine carbamoyltransferase, anabolic; OTCase; EC 2.1.3.3 (characterized)
to candidate WP_011187682.1 DP_RS02175 ornithine carbamoyltransferase

Query= SwissProt::P11724
         (305 letters)



>NCBI__GCF_000025945.1:WP_011187682.1
          Length = 303

 Score =  316 bits (810), Expect = 4e-91
 Identities = 152/296 (51%), Positives = 213/296 (71%), Gaps = 4/296 (1%)

Query: 5   HFLSFMDYSPEELIGLIRRGSELKDLRNRGVLYEPLKSRVLGMVFEKASTRTRLSFEAGM 64
           H  S  D++ EE+  LI R  ELK+ R+RG+ ++ L  + + ++FEK STRTR+SFE+ M
Sbjct: 4   HLSSLGDFTGEEIASLIARAIELKEERSRGIRHQQLAGKSVALIFEKPSTRTRVSFESAM 63

Query: 65  IQLGGQAIFLSPRDTQLGRGEPIGDSARVMSRMLDGVMIRTFAHATLTEFAAHSKVPVIN 124
             LGGQ +FLS RDTQL R EP+ D ARVMSR +DG+++RTF    + E A ++ VPVIN
Sbjct: 64  YGLGGQVLFLSGRDTQLSRSEPLKDMARVMSRYVDGIVVRTFGQEVVNELAQYATVPVIN 123

Query: 125 GLSDDLHPCQLLADMQTFHEHRGSIQGKTVAWIGDGNNMCNSYIEAALKFDFQLRVACPE 184
            L+D  HPCQ+L+D+ T  E +G+IQ   + W+GDGNNM NS+I+AA K  F+L +ACPE
Sbjct: 124 ALTDLHHPCQILSDIMTVIEKKGAIQDLKIVWVGDGNNMANSWIQAAAKLGFELILACPE 183

Query: 185 GYEPKAEFVALA----GDRLRVVRDPREAVAGAHLVSTDVWASMGQEDEAAARIALFRPY 240
           GY+P AE +A A       + ++RDP+ AV GA +++ DV+ASMGQE E   R+ +F  Y
Sbjct: 184 GYDPDAEILAAAQAEGAKPITLLRDPQTAVLGADVINVDVFASMGQESEQDERLKIFASY 243

Query: 241 QVNAALLDGAADDVLFMHCLPAHRGEEISEELLDDPRSVAWDQAENRLHAQKALLE 296
           QVNA ++  AADD + +HCLPAHRGEEI+E++L+ P+ VA+D+AEN++H  KA+LE
Sbjct: 244 QVNAEMMAKAADDAIVLHCLPAHRGEEITEDVLEGPQCVAFDEAENKMHMHKAILE 299


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: 225
Number of extensions: 8
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_011187682.1 DP_RS02175 (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.8180.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.5e-125  403.7   0.0   2.8e-125  403.5   0.0    1.0  1  lcl|NCBI__GCF_000025945.1:WP_011187682.1  DP_RS02175 ornithine carbamoyltr


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000025945.1:WP_011187682.1  DP_RS02175 ornithine carbamoyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  403.5   0.0  2.8e-125  2.8e-125       2     303 ..       4     302 ..       3     303 .] 0.98

  Alignments for each domain:
  == domain 1  score: 403.5 bits;  conditional E-value: 2.8e-125
                                 TIGR00658   2 hllslldlseeelkellelakklkkekkkgkeekklkgktlaliFekrstRtRvsfevaayelGaqvly 70 
                                               hl sl d++ ee+ +l+ +a +lk+e+ +g ++++l gk++aliFek+stRtRvsfe a+y lG+qvl+
  lcl|NCBI__GCF_000025945.1:WP_011187682.1   4 HLSSLGDFTGEEIASLIARAIELKEERSRGIRHQQLAGKSVALIFEKPSTRTRVSFESAMYGLGGQVLF 72 
                                               8899***************************************************************** PP

                                 TIGR00658  71 lnkeelqlgrkesikDtarvlsryvdaivvRvykhedveelakyasvPvingLtdlehPcqilaDllti 139
                                               l+  ++ql+r e++kD arv+sryvd+ivvR++ +e v+ela+ya+vPvin+Ltdl hPcqil+D++t+
  lcl|NCBI__GCF_000025945.1:WP_011187682.1  73 LSGRDTQLSRSEPLKDMARVMSRYVDGIVVRTFGQEVVNELAQYATVPVINALTDLHHPCQILSDIMTV 141
                                               ********************************************************************* PP

                                 TIGR00658 140 keklgklkevklvyvGDannvanslllaaaklGldvvvatPeglepeaeivkkakkiakenggklelte 208
                                               +ek+g+++++k+v+vGD+nn+ans + aaaklG+++ +a+Peg++p+aei+  a++   e    ++l++
  lcl|NCBI__GCF_000025945.1:WP_011187682.1 142 IEKKGAIQDLKIVWVGDGNNMANSWIQAAAKLGFELILACPEGYDPDAEILAAAQA---EGAKPITLLR 207
                                               ***************************************************99965...44456***** PP

                                 TIGR00658 209 dpkkavkdadviytDvwvsmGeeekkeerlkllkpyqvneellelakpevkflhCLPavrGeevtdevl 277
                                               dp+ av +advi  Dv++smG+e++++erlk++  yqvn e+++ a +++++lhCLPa+rGee+t++vl
  lcl|NCBI__GCF_000025945.1:WP_011187682.1 208 DPQTAVLGADVINVDVFASMGQESEQDERLKIFASYQVNAEMMAKAADDAIVLHCLPAHRGEEITEDVL 276
                                               ********************************************************************* PP

                                 TIGR00658 278 egeasivfdeaenRlhaqkavlkall 303
                                               eg++ + fdeaen++h  ka+l+ +l
  lcl|NCBI__GCF_000025945.1:WP_011187682.1 277 EGPQCVAFDEAENKMHMHKAILERFL 302
                                               **********************9877 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: 7.43
//
[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