Alignments for a candidate for arcB in Escherichia coli BW25113

GapMind for catabolism of small carbon sources

Alignments for a candidate for arcB in Escherichia coli BW25113

Align Ornithine carbamoyltransferase subunit F; OTCase-2; EC 2.1.3.3 (characterized)
to candidate 14411 b0273 CP4-6 prophage; ornithine carbamoyltransferase 2, chain F (NCBI)

Query= SwissProt::P06960
         (334 letters)



>FitnessBrowser__Keio:14411
          Length = 334

 Score =  670 bits (1728), Expect = 0.0
 Identities = 334/334 (100%), Positives = 334/334 (100%)

Query: 1   MSDLYKKHFLKLLDFTPAQFTSLLTLAAQLKADKKNGKEVQKLTGKNIALIFEKDSTRTR 60
           MSDLYKKHFLKLLDFTPAQFTSLLTLAAQLKADKKNGKEVQKLTGKNIALIFEKDSTRTR
Sbjct: 1   MSDLYKKHFLKLLDFTPAQFTSLLTLAAQLKADKKNGKEVQKLTGKNIALIFEKDSTRTR 60

Query: 61  CSFEVAAFDQGARVTYLGPSGSQIGHKESIKDTARVLGRMYDGIQYRGHGQEVVETLAQY 120
           CSFEVAAFDQGARVTYLGPSGSQIGHKESIKDTARVLGRMYDGIQYRGHGQEVVETLAQY
Sbjct: 61  CSFEVAAFDQGARVTYLGPSGSQIGHKESIKDTARVLGRMYDGIQYRGHGQEVVETLAQY 120

Query: 121 AGVPVWNGLTNEFHPTQLLADLMTMQEHLPGKAFNEMTLVYAGDARNNMGNSMLEAAALT 180
           AGVPVWNGLTNEFHPTQLLADLMTMQEHLPGKAFNEMTLVYAGDARNNMGNSMLEAAALT
Sbjct: 121 AGVPVWNGLTNEFHPTQLLADLMTMQEHLPGKAFNEMTLVYAGDARNNMGNSMLEAAALT 180

Query: 181 GLDLRLLAPKACWPEESLVAECSALAEKHGGKITLTEDVAAGVKGADFIYTDVWVSMGEA 240
           GLDLRLLAPKACWPEESLVAECSALAEKHGGKITLTEDVAAGVKGADFIYTDVWVSMGEA
Sbjct: 181 GLDLRLLAPKACWPEESLVAECSALAEKHGGKITLTEDVAAGVKGADFIYTDVWVSMGEA 240

Query: 241 KEKWAERIALLRGYQVNAQMMALTDNPNVKFLHCLPAFHDDQTTLGKQMAKEFDLHGGME 300
           KEKWAERIALLRGYQVNAQMMALTDNPNVKFLHCLPAFHDDQTTLGKQMAKEFDLHGGME
Sbjct: 241 KEKWAERIALLRGYQVNAQMMALTDNPNVKFLHCLPAFHDDQTTLGKQMAKEFDLHGGME 300

Query: 301 VTDEVFESAASIVFDQAENRMHTIKAVMMATLGE 334
           VTDEVFESAASIVFDQAENRMHTIKAVMMATLGE
Sbjct: 301 VTDEVFESAASIVFDQAENRMHTIKAVMMATLGE 334


Lambda     K      H
   0.318    0.132    0.385 

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: 554
Number of extensions: 15
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: 334
Length of database: 334
Length adjustment: 28
Effective length of query: 306
Effective length of database: 306
Effective search space:    93636
Effective search space used:    93636
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: 49 (23.5 bits)

Align candidate 14411 b0273 (CP4-6 prophage; ornithine carbamoyltransferase 2, chain F (NCBI))
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.4757.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   3.5e-139  449.1   0.0     4e-139  448.9   0.0    1.0  1  lcl|FitnessBrowser__Keio:14411  b0273 CP4-6 prophage; ornithine 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Keio:14411  b0273 CP4-6 prophage; ornithine carbamoyltransferase 2, chain F (NCBI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  448.9   0.0    4e-139    4e-139       1     303 [.       7     332 ..       7     333 .. 0.99

  Alignments for each domain:
  == domain 1  score: 448.9 bits;  conditional E-value: 4e-139
                       TIGR00658   1 rhllslldlseeelkellelakklkkekkkgkeekklkgktlaliFekrstRtRvsfevaayelGaqvlylnkeelqlg 79 
                                     +h+l+lld++++++++ll la++lk++kk+gke +kl+gk++aliFek+stRtR+sfevaa+++Ga+v+yl+++ +q+g
  lcl|FitnessBrowser__Keio:14411   7 KHFLKLLDFTPAQFTSLLTLAAQLKADKKNGKEVQKLTGKNIALIFEKDSTRTRCSFEVAAFDQGARVTYLGPSGSQIG 85 
                                     79***************************************************************************** PP

                       TIGR00658  80 rkesikDtarvlsryvdaivvRvykhedveelakyasvPvingLtdlehPcqilaDlltikeklg..klkevklvyvGD 156
                                     +kesikDtarvl+r++d+i++R++ +e ve+la+ya+vPv+ngLt+++hP+q+laDl+t++e+l   +++e++lvy GD
  lcl|FitnessBrowser__Keio:14411  86 HKESIKDTARVLGRMYDGIQYRGHGQEVVETLAQYAGVPVWNGLTNEFHPTQLLADLMTMQEHLPgkAFNEMTLVYAGD 164
                                     ****************************************************************8889*********** PP

                       TIGR00658 157 a.nnvanslllaaaklGldvvvatPeglepeaeivkkakkiakenggkleltedpkkavkdadviytDvwvsmGe.eek 233
                                     a nn++ns+l aaa++Gld+++ +P++++pe+++v +++++a+++ggk++lted++ +vk+ad+iytDvwvsmGe +ek
  lcl|FitnessBrowser__Keio:14411 165 ArNNMGNSMLEAAALTGLDLRLLAPKACWPEESLVAECSALAEKHGGKITLTEDVAAGVKGADFIYTDVWVSMGEaKEK 243
                                     ***************************************************************************9999 PP

                       TIGR00658 234 keerlkllkpyqvneellela.kpevkflhCLPavr..................GeevtdevlegeasivfdeaenRlh 293
                                     ++er++ll++yqvn ++++l+ +p+vkflhCLPa++                  G+evtdev+e++asivfd+aenR+h
  lcl|FitnessBrowser__Keio:14411 244 WAERIALLRGYQVNAQMMALTdNPNVKFLHCLPAFHddqttlgkqmakefdlhgGMEVTDEVFESAASIVFDQAENRMH 322
                                     *********************99******************************************************** PP

                       TIGR00658 294 aqkavlkall 303
                                     ++kav+ a+l
  lcl|FitnessBrowser__Keio:14411 323 TIKAVMMATL 332
                                     ******9988 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (304 nodes)
Target sequences:                          1  (334 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: 8.02
//
[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:

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

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 catabolism of small carbon sources