Alignments for a candidate for argI in Desulfotomaculum ruminis DSM 2154

GapMind for Amino acid biosynthesis

Alignments for a candidate for argI in Desulfotomaculum ruminis DSM 2154

Align ornithine carbamoyltransferase (EC 2.1.3.3) (characterized)
to candidate WP_013840424.1 DESRU_RS01835 ornithine carbamoyltransferase

Query= BRENDA::O93656
         (317 letters)



>NCBI__GCF_000215085.1:WP_013840424.1
          Length = 313

 Score =  393 bits (1009), Expect = e-114
 Identities = 190/306 (62%), Positives = 243/306 (79%)

Query: 5   LKGRDLLCLQDYTPEEIWTILETAKMLKIWQKIGKPHRLLEGKTLAMIFQKPSTRTRVSF 64
           LKG+D L L D++ EE+  +L+ A  +K  QK G PH  L GKTLAMIFQK STRTRVSF
Sbjct: 8   LKGKDFLTLHDFSVEEVQFMLDEAVRIKGLQKSGIPHPYLRGKTLAMIFQKSSTRTRVSF 67

Query: 65  EVAMAHLGGHALYLNAQDLQLRRGETIADTARVLSRYVDAIMARVYDHKDVEDLAKYASV 124
           EVAM  LGG+AL+L+ +D+Q+ RGE+IADTARVLSR+VD IM R Y    VE+LA YA+V
Sbjct: 68  EVAMVQLGGYALFLSPKDIQMGRGESIADTARVLSRFVDGIMIRTYAQSQVEELAHYATV 127

Query: 125 PVINGLSDFSHPCQALADYMTIWEKKGTIKGVKVVYVGDGNNVAHSLMIAGTKLGADVVV 184
           PVINGL+D +HPCQ LAD++TI E KG + G+++ YVGDGNN+AHSLM    K+G ++ +
Sbjct: 128 PVINGLTDLTHPCQILADFLTIKEHKGRLAGLRLAYVGDGNNIAHSLMYGCAKVGMNISI 187

Query: 185 ATPEGYEPDEKVIKWAEQNAAESGGSFELLHDPVKAVKDADVIYTDVWASMGQEAEAEER 244
           A+PEGY+PD+KV++ A+Q+A  +G   E++ DPV+AV  ADV+ TDVW SMGQEAE + R
Sbjct: 188 ASPEGYKPDQKVVELAKQDALATGARIEIVTDPVQAVTGADVVVTDVWTSMGQEAEYDLR 247

Query: 245 RKIFRPFQVNKDLVKHAKPDYMFMHCLPAHRGEEVTDDVIDSPNSVVWDEAENRLHAQKA 304
           +KIF P+Q+NK+L   AK DY+ +HCLPAHRGEEVTD++ID P+S VWDEAENRLHAQKA
Sbjct: 248 KKIFAPYQLNKELCALAKEDYISLHCLPAHRGEEVTDEIIDGPHSAVWDEAENRLHAQKA 307

Query: 305 VLALLL 310
           VLALL+
Sbjct: 308 VLALLM 313


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: 338
Number of extensions: 12
Number of successful extensions: 1
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: 313
Length adjustment: 27
Effective length of query: 290
Effective length of database: 286
Effective search space:    82940
Effective search space used:    82940
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 WP_013840424.1 DESRU_RS01835 (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.1951.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.8e-137  443.5   0.0     2e-137  443.3   0.0    1.0  1  lcl|NCBI__GCF_000215085.1:WP_013840424.1  DESRU_RS01835 ornithine carbamoy


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000215085.1:WP_013840424.1  DESRU_RS01835 ornithine carbamoyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  443.3   0.0    2e-137    2e-137       1     303 [.      11     313 .]      11     313 .] 0.99

  Alignments for each domain:
  == domain 1  score: 443.3 bits;  conditional E-value: 2e-137
                                 TIGR00658   1 rhllslldlseeelkellelakklkkekkkgkeekklkgktlaliFekrstRtRvsfevaayelGaqvl 69 
                                               +++l+l+d+s ee++ +l+ a ++k  +k+g  + +l+gktla+iF+k+stRtRvsfeva+++lG+ +l
  lcl|NCBI__GCF_000215085.1:WP_013840424.1  11 KDFLTLHDFSVEEVQFMLDEAVRIKGLQKSGIPHPYLRGKTLAMIFQKSSTRTRVSFEVAMVQLGGYAL 79 
                                               79******************************************************************* PP

                                 TIGR00658  70 ylnkeelqlgrkesikDtarvlsryvdaivvRvykhedveelakyasvPvingLtdlehPcqilaDllt 138
                                               +l+++++q+gr+esi+Dtarvlsr+vd+i++R+y++++veela+ya+vPvingLtdl+hPcqilaD+lt
  lcl|NCBI__GCF_000215085.1:WP_013840424.1  80 FLSPKDIQMGRGESIADTARVLSRFVDGIMIRTYAQSQVEELAHYATVPVINGLTDLTHPCQILADFLT 148
                                               ********************************************************************* PP

                                 TIGR00658 139 ikeklgklkevklvyvGDannvanslllaaaklGldvvvatPeglepeaeivkkakkiakenggklelt 207
                                               ike++g+l +++l+yvGD+nn+a+sl+ ++ak+G+++++a+Peg++p++++v+ ak+ a ++g+++e++
  lcl|NCBI__GCF_000215085.1:WP_013840424.1 149 IKEHKGRLAGLRLAYVGDGNNIAHSLMYGCAKVGMNISIASPEGYKPDQKVVELAKQDALATGARIEIV 217
                                               ********************************************************************* PP

                                 TIGR00658 208 edpkkavkdadviytDvwvsmGeeekkeerlkllkpyqvneellelakpevkflhCLPavrGeevtdev 276
                                                dp++av++adv++tDvw+smG+e++ + r k++ pyq+n+el +lak++++ lhCLPa+rGeevtde+
  lcl|NCBI__GCF_000215085.1:WP_013840424.1 218 TDPVQAVTGADVVVTDVWTSMGQEAEYDLRKKIFAPYQLNKELCALAKEDYISLHCLPAHRGEEVTDEI 286
                                               ********************************************************************* PP

                                 TIGR00658 277 legeasivfdeaenRlhaqkavlkall 303
                                               ++g++s v+deaenRlhaqkavl++l+
  lcl|NCBI__GCF_000215085.1:WP_013840424.1 287 IDGPHSAVWDEAENRLHAQKAVLALLM 313
                                               ***********************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (304 nodes)
Target sequences:                          1  (313 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 7.15
//
[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