GapMind for catabolism of small carbon sources

 

Aligments for a candidate for arcB in Shewanella loihica PV-4

Align Ornithine carbamoyltransferase; OTCase; EC 2.1.3.3 (characterized)
to candidate 5207682 Shew_0204 ornithine carbamoyltransferase (RefSeq)

Query= SwissProt::Q9K4Y9
         (301 letters)



>lcl|FitnessBrowser__PV4:5207682 Shew_0204 ornithine
           carbamoyltransferase (RefSeq)
          Length = 301

 Score =  389 bits (1000), Expect = e-113
 Identities = 180/300 (60%), Positives = 242/300 (80%)

Query: 1   MENLLSVKDLSKQQILDLLALAKAVKANPAEYSQALAGKSIVTIYEKPSLRTRVTFDIGI 60
           M +LLS+K+L++QQ++DLLALAK +KANP +Y +AL GKS+V ++EKPSLRTRV+FDIGI
Sbjct: 1   MNHLLSIKELTQQQLIDLLALAKTIKANPEDYRKALDGKSVVMLFEKPSLRTRVSFDIGI 60

Query: 61  HKLGGHAVYLDAQNGAIGERETVKDFAANISRWADAIVARVVSHKTLEGLVEHGSVPVVN 120
           +KLGGH +YLD QNGA+G+RE V DFAANIS WADAIVAR  +H T+E L EHG+VPV+N
Sbjct: 61  NKLGGHCLYLDQQNGALGKREPVSDFAANISCWADAIVARTFAHSTIEQLAEHGTVPVIN 120

Query: 121 SLCDLYHPCQALADFLTISEHYEDVSKVKLAYVGEGNNVTHSLMLTGAILGAEVTAVCPR 180
           +L D+YHPCQ LADFLT++E ++DVSKVKLAYVG+GNNVTHSLM   A+LGA++T +CP+
Sbjct: 121 ALSDMYHPCQGLADFLTLAEQFDDVSKVKLAYVGDGNNVTHSLMYGAALLGAKMTVICPQ 180

Query: 181 GSSPDAQIVKQAMALAEISGGKINVTDNLDDIVDYDVIYGDTWVSMGDDTPLAQVKEKYM 240
           G  PD ++V +A A+AE  GG++ ++ +++ I  +D IY DTW+SMGD   L ++K K+ 
Sbjct: 181 GHFPDGKVVLEAQAIAEAHGGELVLSSDVEAIAGHDAIYTDTWISMGDKASLDEIKAKFA 240

Query: 241 PYQINKALLMRTGIKHVLHCQPAHRELEITSEVMDGEHSLIFDQAENRMHAQNAVLLTLL 300
           PY ++  ++ + G K  +HC PA+R +E+ +EV+DG  SLI  QAENRMHAQNAVL+TLL
Sbjct: 241 PYHVDTDMMNKAGAKFFMHCLPAYRGVEVAAEVVDGAGSLILQQAENRMHAQNAVLVTLL 300


Lambda     K      H
   0.317    0.133    0.379 

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: 261
Number of extensions: 6
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: 301
Length of database: 301
Length adjustment: 27
Effective length of query: 274
Effective length of database: 274
Effective search space:    75076
Effective search space used:    75076
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 48 (23.1 bits)

Align candidate 5207682 Shew_0204 (ornithine carbamoyltransferase (RefSeq))
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.5617.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                        -----------
   1.1e-104  335.8   0.0   1.2e-104  335.7   0.0    1.0  1  lcl|FitnessBrowser__PV4:5207682  Shew_0204 ornithine carbamoyltra


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PV4:5207682  Shew_0204 ornithine carbamoyltransferase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  335.7   0.0  1.2e-104  1.2e-104       2     303 ..       3     300 ..       2     301 .] 0.98

  Alignments for each domain:
  == domain 1  score: 335.7 bits;  conditional E-value: 1.2e-104
                        TIGR00658   2 hllslldlseeelkellelakklkkekkkgkeekklkgktlaliFekrstRtRvsfevaayelGaqvlylnkeelqlg 79 
                                      hlls+++l++++l +ll lak++k++ +    +k l gk++ ++Fek+s RtRvsf++++ +lG++ lyl++++  lg
  lcl|FitnessBrowser__PV4:5207682   3 HLLSIKELTQQQLIDLLALAKTIKANPED--YRKALDGKSVVMLFEKPSLRTRVSFDIGINKLGGHCLYLDQQNGALG 78 
                                      9************************9998..6889******************************************* PP

                        TIGR00658  80 rkesikDtarvlsryvdaivvRvykhedveelakyasvPvingLtdlehPcqilaDlltikeklgklkevklvyvGDa 157
                                      ++e+++D a  +s + daiv+R+++h+++e+la++ +vPvin+L+d+ hPcq laD+lt+ e+++++++vkl+yvGD+
  lcl|FitnessBrowser__PV4:5207682  79 KREPVSDFAANISCWADAIVARTFAHSTIEQLAEHGTVPVINALSDMYHPCQGLADFLTLAEQFDDVSKVKLAYVGDG 156
                                      ****************************************************************************** PP

                        TIGR00658 158 nnvanslllaaaklGldvvvatPeglepeaeivkkakkiakenggkleltedpkkavkdadviytDvwvsmGeeekke 235
                                      nnv++sl+ +aa+lG +++v +P+g  p+ ++v +a++ia+++gg+l l +d+ +a+++ d iytD+w+smG++++ +
  lcl|FitnessBrowser__PV4:5207682 157 NNVTHSLMYGAALLGAKMTVICPQGHFPDGKVVLEAQAIAEAHGGELVLSSDV-EAIAGHDAIYTDTWISMGDKASLD 233
                                      ***********************************************999996.79********************** PP

                        TIGR00658 236 erlkllkpyqvneellelakpevkflhCLPavrGeevtdevlegeasivfdeaenRlhaqkavlkall 303
                                      e  + + py v++++++ a  +  f+hCLPa rG ev+ ev++g+ s++ ++aenR+haq avl++ll
  lcl|FitnessBrowser__PV4:5207682 234 EIKAKFAPYHVDTDMMNKAGAK-FFMHCLPAYRGVEVAAEVVDGAGSLILQQAENRMHAQNAVLVTLL 300
                                      *****************99765.69***************************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (304 nodes)
Target sequences:                          1  (301 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: 7.10
//
[ok]

This GapMind analysis is from Sep 17 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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