GapMind for catabolism of small carbon sources

 

Alignments for a candidate for arcB in Desulfacinum infernum DSM 9756

Align ornithine carbamoyltransferase (EC 2.1.3.3) (characterized)
to candidate WP_073039304.1 BUB04_RS11055 ornithine carbamoyltransferase

Query= BRENDA::O93656
         (317 letters)



>NCBI__GCF_900129305.1:WP_073039304.1
          Length = 307

 Score =  318 bits (816), Expect = 8e-92
 Identities = 160/303 (52%), Positives = 216/303 (71%), Gaps = 3/303 (0%)

Query: 8   RDLLCLQDYTPEEIWTILETAKMLKIWQKIGKPHRLLEGKTLAMIFQKPSTRTRVSFEVA 67
           RD L L D   +E+  +L+ A  LK     G    +L+ KTL MIF KPSTRTRVSFE A
Sbjct: 3   RDFLSLWDVNADELNHLLDLAGRLKAEWAAGTLRPVLQQKTLGMIFSKPSTRTRVSFEAA 62

Query: 68  MAHLGGHALYLNAQDLQLRRGETIADTARVLSRYVDAIMARVYDHKDVEDLAKYASVPVI 127
           M  LGG+  +++ QD Q+ R E ++DTARVLSRY+ A++ R Y  ++VE LA+YAS+PVI
Sbjct: 63  MHRLGGNCTFMSVQDTQISRAEPLSDTARVLSRYIHALVVRTYAQEEVETLAQYASIPVI 122

Query: 128 NGLSDFSHPCQALADYMTIWEKKGTIKGVKVVYVGDGNNVAHSLMIAGTKLGADVVVATP 187
           NGL+D  HPCQ L+D +TI EK+G++ G+ V ++GDGNN+AHS + A  +LG  + +A P
Sbjct: 123 NGLTDLYHPCQVLSDLLTIREKRGSLDGMVVAWIGDGNNMAHSWINASARLGFRLNIACP 182

Query: 188 EGYEPDEKVIKWAEQNAAESGGSFELLHDPVKAVKDADVIYTDVWASMGQEAEAEERRKI 247
           EGY P  +VI   E+   E      L  DP +AV++ADVI TDVWASMGQE+EA  RR +
Sbjct: 183 EGYWPSARVI---ERARTEGAAPIRLFDDPRQAVEEADVINTDVWASMGQESEAATRRAL 239

Query: 248 FRPFQVNKDLVKHAKPDYMFMHCLPAHRGEEVTDDVIDSPNSVVWDEAENRLHAQKAVLA 307
           F+PFQVN++L+++A    M +HCLPAHRGEE+T++V++ P SVV+D+AENRLHAQ A+L 
Sbjct: 240 FQPFQVNRELLRYAPSHAMVLHCLPAHRGEEITEEVLEGPQSVVFDQAENRLHAQAALLY 299

Query: 308 LLL 310
            LL
Sbjct: 300 WLL 302


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: 291
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: 307
Length adjustment: 27
Effective length of query: 290
Effective length of database: 280
Effective search space:    81200
Effective search space used:    81200
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_073039304.1 BUB04_RS11055 (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.carbon/TIGR00658.hmm
# target sequence database:        /tmp/gapView.1804690.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   4.8e-126  406.0   0.0   5.5e-126  405.8   0.0    1.0  1  NCBI__GCF_900129305.1:WP_073039304.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900129305.1:WP_073039304.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  405.8   0.0  5.5e-126  5.5e-126       1     303 [.       3     302 ..       3     303 .. 0.99

  Alignments for each domain:
  == domain 1  score: 405.8 bits;  conditional E-value: 5.5e-126
                             TIGR00658   1 rhllslldlseeelkellelakklkkekkkgkeekklkgktlaliFekrstRtRvsfevaayelGaqvlylnk 73 
                                           r++lsl+d++ +el++ll+la +lk+e  +g+ +  l++ktl++iF k+stRtRvsfe+a+ +lG++ ++++ 
  NCBI__GCF_900129305.1:WP_073039304.1   3 RDFLSLWDVNADELNHLLDLAGRLKAEWAAGTLRPVLQQKTLGMIFSKPSTRTRVSFEAAMHRLGGNCTFMSV 75 
                                           79*********************************************************************** PP

                             TIGR00658  74 eelqlgrkesikDtarvlsryvdaivvRvykhedveelakyasvPvingLtdlehPcqilaDlltikeklgkl 146
                                           +++q++r e+++Dtarvlsry++a+vvR+y++e+ve+la+yas+PvingLtdl hPcq+l+Dllti+ek g+l
  NCBI__GCF_900129305.1:WP_073039304.1  76 QDTQISRAEPLSDTARVLSRYIHALVVRTYAQEEVETLAQYASIPVINGLTDLYHPCQVLSDLLTIREKRGSL 148
                                           ************************************************************************* PP

                             TIGR00658 147 kevklvyvGDannvanslllaaaklGldvvvatPeglepeaeivkkakkiakenggkleltedpkkavkdadv 219
                                           +++ ++++GD+nn+a+s + a+a lG+ +++a+Peg++p+a+++++a+    e  + ++l +dp +av++adv
  NCBI__GCF_900129305.1:WP_073039304.1 149 DGMVVAWIGDGNNMAHSWINASARLGFRLNIACPEGYWPSARVIERART---EGAAPIRLFDDPRQAVEEADV 218
                                           ***********************************************76...77799**************** PP

                             TIGR00658 220 iytDvwvsmGeeekkeerlkllkpyqvneellelakpevkflhCLPavrGeevtdevlegeasivfdeaenRl 292
                                           i tDvw+smG+e++++ r +l++p+qvn+ell++a +++++lhCLPa+rGee+t+evleg++s+vfd+aenRl
  NCBI__GCF_900129305.1:WP_073039304.1 219 INTDVWASMGQESEAATRRALFQPFQVNRELLRYAPSHAMVLHCLPAHRGEEITEEVLEGPQSVVFDQAENRL 291
                                           ************************************************************************* PP

                             TIGR00658 293 haqkavlkall 303
                                           haq a+l +ll
  NCBI__GCF_900129305.1:WP_073039304.1 292 HAQAALLYWLL 302
                                           ******99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (304 nodes)
Target sequences:                          1  (307 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: 21.24
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

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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:

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:

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:

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:

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