Alignments for a candidate for argI in Shewanella oneidensis MR-1

GapMind for Amino acid biosynthesis

Alignments for a candidate for argI in Shewanella oneidensis MR-1

Align Ornithine carbamoyltransferase; OTCase; EC 2.1.3.3 (characterized)
to candidate 199472 SO0277 ornithine carbamoyltransferase (NCBI ptt file)

Query= SwissProt::Q9K4Y9
         (301 letters)



>FitnessBrowser__MR1:199472
          Length = 301

 Score =  399 bits (1024), Expect = e-116
 Identities = 188/299 (62%), Positives = 239/299 (79%)

Query: 1   MENLLSVKDLSKQQILDLLALAKAVKANPAEYSQALAGKSIVTIYEKPSLRTRVTFDIGI 60
           M++ LS+K+L++QQ+LDL+ LAK +KANPAEY  AL GKS+V ++EKPSLRTRV+FDIGI
Sbjct: 1   MKHFLSIKELTQQQLLDLITLAKTIKANPAEYRHALDGKSVVMLFEKPSLRTRVSFDIGI 60

Query: 61  HKLGGHAVYLDAQNGAIGERETVKDFAANISRWADAIVARVVSHKTLEGLVEHGSVPVVN 120
           +K GGH +YLD QNGA+G+RE+V DFA+N+S WADAIVAR  SH T+E L E G+VPV+N
Sbjct: 61  NKFGGHCLYLDQQNGALGKRESVADFASNLSCWADAIVARTYSHTTIEQLAEFGTVPVIN 120

Query: 121 SLCDLYHPCQALADFLTISEHYEDVSKVKLAYVGEGNNVTHSLMLTGAILGAEVTAVCPR 180
           +L DLYHPCQALADFLT++EH+E++S VKLAYVG+GNNVT+SLM   AILGA +T +CP 
Sbjct: 121 ALSDLYHPCQALADFLTLAEHFENISDVKLAYVGDGNNVTNSLMYCAAILGATMTVICPA 180

Query: 181 GSSPDAQIVKQAMALAEISGGKINVTDNLDDIVDYDVIYGDTWVSMGDDTPLAQVKEKYM 240
           G  PD  +V +   LA   GGKI +T ++D I  +D IY DTW+SMGD TPLA++K+K+ 
Sbjct: 181 GHFPDGYVVAEVQELASRYGGKIVLTSDIDAIEGHDAIYTDTWISMGDPTPLAEIKDKFA 240

Query: 241 PYQINKALLMRTGIKHVLHCQPAHRELEITSEVMDGEHSLIFDQAENRMHAQNAVLLTL 299
           PYQ+N AL+ + G    +HC PAHR +E+T  VMDGE SLI  QAENRMHAQNAVL+TL
Sbjct: 241 PYQVNNALMAKAGAHFFMHCLPAHRGVEVTDAVMDGECSLILQQAENRMHAQNAVLVTL 299


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: 274
Number of extensions: 2
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 199472 SO0277 (ornithine carbamoyltransferase (NCBI ptt file))
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.24924.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   1.2e-108  348.8   0.0   1.4e-108  348.6   0.0    1.0  1  lcl|FitnessBrowser__MR1:199472  SO0277 ornithine carbamoyltransf


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__MR1:199472  SO0277 ornithine carbamoyltransferase (NCBI ptt file)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  348.6   0.0  1.4e-108  1.4e-108       1     303 [.       2     300 ..       2     301 .] 0.98

  Alignments for each domain:
  == domain 1  score: 348.6 bits;  conditional E-value: 1.4e-108
                       TIGR00658   1 rhllslldlseeelkellelakklkkekkkgkeekklkgktlaliFekrstRtRvsfevaayelGaqvlylnkeelqlg 79 
                                     +h+ls+++l++++l +l+ lak++k++  +   ++ l gk++ ++Fek+s RtRvsf++++ ++G++ lyl++++  lg
  lcl|FitnessBrowser__MR1:199472   2 KHFLSIKELTQQQLLDLITLAKTIKANPAE--YRHALDGKSVVMLFEKPSLRTRVSFDIGINKFGGHCLYLDQQNGALG 78 
                                     79************************9998..5668******************************************* PP

                       TIGR00658  80 rkesikDtarvlsryvdaivvRvykhedveelakyasvPvingLtdlehPcqilaDlltikeklgklkevklvyvGDan 158
                                     ++es++D a  ls + daiv+R+y+h+++e+la++ +vPvin+L+dl hPcq+laD+lt+ e+++++++vkl+yvGD+n
  lcl|FitnessBrowser__MR1:199472  79 KRESVADFASNLSCWADAIVARTYSHTTIEQLAEFGTVPVINALSDLYHPCQALADFLTLAEHFENISDVKLAYVGDGN 157
                                     ******************************************************************************* PP

                       TIGR00658 159 nvanslllaaaklGldvvvatPeglepeaeivkkakkiakenggkleltedpkkavkdadviytDvwvsmGeeekkeer 237
                                     nv+nsl+  aa lG +++v +P g  p+  +v + +++a+++ggk+ lt+d+ +a+++ d iytD+w+smG+ +  +e 
  lcl|FitnessBrowser__MR1:199472 158 NVTNSLMYCAAILGATMTVICPAGHFPDGYVVAEVQELASRYGGKIVLTSDI-DAIEGHDAIYTDTWISMGDPTPLAEI 235
                                     ***************************************************8.69*********************9** PP

                       TIGR00658 238 lkllkpyqvneellelakpevkflhCLPavrGeevtdevlegeasivfdeaenRlhaqkavlkall 303
                                      + + pyqvn+ l++ a     f+hCLPa+rG evtd v++ge s++ ++aenR+haq avl++l+
  lcl|FitnessBrowser__MR1:199472 236 KDKFAPYQVNNALMAKAGA-HFFMHCLPAHRGVEVTDAVMDGECSLILQQAENRMHAQNAVLVTLF 300
                                     **************99865.57****************************************9886 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 9.50
//
[ok]

This GapMind analysis is from Apr 09 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