GapMind for catabolism of small carbon sources

 

Alignments for a candidate for arcB in Pontimonas salivibrio CL-TW6

Align ornithine carbamoyltransferase (EC 2.1.3.3) (characterized)
to candidate WP_104913671.1 C3B54_RS05910 ornithine carbamoyltransferase

Query= BRENDA::P0A5M9
         (307 letters)



>NCBI__GCF_002950575.1:WP_104913671.1
          Length = 307

 Score =  354 bits (909), Expect = e-102
 Identities = 177/307 (57%), Positives = 222/307 (72%)

Query: 1   MIRHFLRDDDLSPAEQAEVLELAAELKKDPVSRRPLQGPRGVAVIFDKNSTRTRFSFELG 60
           M RHFLRDDD++P EQAE+L LA ++K      RPL+GP+ VAVIFDK+STRTR SF +G
Sbjct: 1   MTRHFLRDDDVTPEEQAEILSLAGQMKAQRFEHRPLEGPQTVAVIFDKSSTRTRVSFAVG 60

Query: 61  IAQLGGHAVVVDSGSTQLGRDETLQDTAKVLSRYVDAIVWRTFGQERLDAMASVATVPVI 120
           IA LGG  +++ + S+QLG  ET  DTA+VL R V AIVWRT+GQE L+ MA   TVPV+
Sbjct: 61  IADLGGTPLIISTASSQLGGKETPADTARVLERMVAAIVWRTYGQEGLEEMADGTTVPVV 120

Query: 121 NALSDEFHPCQVLADLQTIAERKGALRGLRLSYFGDGANNMAHSLLLGGVTAGIHVTVAA 180
           NALSD+FHPCQ+LADL T+ E+ G L+   + + GDG +NMA S LL    AG+HV +A 
Sbjct: 121 NALSDDFHPCQLLADLLTMQEKLGTLQDRVVCFSGDGRSNMAQSYLLACAAAGMHVRIAC 180

Query: 181 PEGFLPDPSVRAAAERRAQDTGASVTVTADAHAAAAGADVLVTDTWTSMGQENDGLDRVK 240
           PE F P   V A AER A  TG SV V  D     AGADV+VTDTW SMG+E++ + RVK
Sbjct: 181 PEQFAPRADVVADAERIALQTGGSVRVGVDPEELVAGADVVVTDTWVSMGKEDEKVQRVK 240

Query: 241 PFRPFQLNSRLLALADSDAIVLHCLPAHRGDEITDAVMDGPASAVWDEAENRLHAQKALL 300
            F P+Q+  +L+ALA   A+ +HCLPA RG E+  +V+DGP S +WDE+ENRLHAQKALL
Sbjct: 241 TFTPYQVTDQLMALAKPGALFMHCLPADRGFEVEQSVIDGPQSVIWDESENRLHAQKALL 300

Query: 301 VWLLERS 307
            WLLER+
Sbjct: 301 AWLLERA 307


Lambda     K      H
   0.319    0.133    0.387 

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: 270
Number of extensions: 9
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: 307
Length of database: 307
Length adjustment: 27
Effective length of query: 280
Effective length of database: 280
Effective search space:    78400
Effective search space used:    78400
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 (21.8 bits)
S2: 48 (23.1 bits)

Align candidate WP_104913671.1 C3B54_RS05910 (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.714882.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   6.8e-114  366.1   0.0   7.7e-114  365.9   0.0    1.0  1  NCBI__GCF_002950575.1:WP_104913671.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_002950575.1:WP_104913671.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  365.9   0.0  7.7e-114  7.7e-114       1     303 [.       3     304 ..       3     305 .. 0.99

  Alignments for each domain:
  == domain 1  score: 365.9 bits;  conditional E-value: 7.7e-114
                             TIGR00658   1 rhllslldlseeelkellelakklkkekkkgkeekklkg.ktlaliFekrstRtRvsfevaayelGaqvlyln 72 
                                           rh+l   d+++ee  e+l la ++k+++ +   ++ l+g +t+a+iF+k+stRtRvsf v++++lG+ +l+++
  NCBI__GCF_002950575.1:WP_104913671.1   3 RHFLRDDDVTPEEQAEILSLAGQMKAQRFE---HRPLEGpQTVAVIFDKSSTRTRVSFAVGIADLGGTPLIIS 72 
                                           799999*******************99988...899998689******************************* PP

                             TIGR00658  73 keelqlgrkesikDtarvlsryvdaivvRvykhedveelakyasvPvingLtdlehPcqilaDlltikeklgk 145
                                           + ++qlg ke+ +Dtarvl+r+v aiv R+y +e +ee+a+ ++vPv+n+L+d +hPcq+laDllt++eklg+
  NCBI__GCF_002950575.1:WP_104913671.1  73 TASSQLGGKETPADTARVLERMVAAIVWRTYGQEGLEEMADGTTVPVVNALSDDFHPCQLLADLLTMQEKLGT 145
                                           ************************************************************************* PP

                             TIGR00658 146 lkevklvyvGDa.nnvanslllaaaklGldvvvatPeglepeaeivkkakkiakenggkleltedpkkavkda 217
                                           l++  + + GD+  n+a+s lla+a  G++v++a+Pe++ p+a++v  a++ia ++gg++++  dp++ v++a
  NCBI__GCF_002950575.1:WP_104913671.1 146 LQDRVVCFSGDGrSNMAQSYLLACAAAGMHVRIACPEQFAPRADVVADAERIALQTGGSVRVGVDPEELVAGA 218
                                           ************9************************************************************ PP

                             TIGR00658 218 dviytDvwvsmGeeekkeerlkllkpyqvneellelakpevkflhCLPavrGeevtdevlegeasivfdeaen 290
                                           dv++tD+wvsmG+e++k +r+k + pyqv+++l++lakp + f+hCLPa rG ev + v++g++s+++de en
  NCBI__GCF_002950575.1:WP_104913671.1 219 DVVVTDTWVSMGKEDEKVQRVKTFTPYQVTDQLMALAKPGALFMHCLPADRGFEVEQSVIDGPQSVIWDESEN 291
                                           ************************************************************************* PP

                             TIGR00658 291 Rlhaqkavlkall 303
                                           Rlhaqka+l++ll
  NCBI__GCF_002950575.1:WP_104913671.1 292 RLHAQKALLAWLL 304
                                           **********998 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: 16.19
//
[ok]

This GapMind analysis is from Sep 24 2021. 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