GapMind for catabolism of small carbon sources

 

Aligments for a candidate for arcB in Klebsiella michiganensis M5al

Align Ornithine carbamoyltransferase subunit F; OTCase-2; EC 2.1.3.3 (characterized)
to candidate BWI76_RS03010 BWI76_RS03010 ornithine carbamoyltransferase

Query= SwissProt::P06960
         (334 letters)



>lcl|FitnessBrowser__Koxy:BWI76_RS03010 BWI76_RS03010 ornithine
           carbamoyltransferase
          Length = 334

 Score =  608 bits (1569), Expect = e-179
 Identities = 299/334 (89%), Positives = 317/334 (94%)

Query: 1   MSDLYKKHFLKLLDFTPAQFTSLLTLAAQLKADKKNGKEVQKLTGKNIALIFEKDSTRTR 60
           MS  Y+KHFLKLLDFTPA+ T+LL LAA+LKADKKN  E+Q LTGKNIALIFEKDSTRTR
Sbjct: 1   MSAFYQKHFLKLLDFTPAEITALLELAARLKADKKNNIEIQHLTGKNIALIFEKDSTRTR 60

Query: 61  CSFEVAAFDQGARVTYLGPSGSQIGHKESIKDTARVLGRMYDGIQYRGHGQEVVETLAQY 120
           CSFEVAAFDQGARVTYLGPSGSQIGHKESIKDTARVLGRMYDGIQYRGHGQEVVETLA+Y
Sbjct: 61  CSFEVAAFDQGARVTYLGPSGSQIGHKESIKDTARVLGRMYDGIQYRGHGQEVVETLAEY 120

Query: 121 AGVPVWNGLTNEFHPTQLLADLMTMQEHLPGKAFNEMTLVYAGDARNNMGNSMLEAAALT 180
           AGVPVWNGLTNEFHPTQLLADL+TMQEHLPGKAFN+MTLVYAGDARNNMGNSMLEAAALT
Sbjct: 121 AGVPVWNGLTNEFHPTQLLADLLTMQEHLPGKAFNQMTLVYAGDARNNMGNSMLEAAALT 180

Query: 181 GLDLRLLAPKACWPEESLVAECSALAEKHGGKITLTEDVAAGVKGADFIYTDVWVSMGEA 240
           GLDLRL+AP ACWPEE LV +C ALA+K+GG ITLTED+AAGVKGADFIYTDVWVSMGEA
Sbjct: 181 GLDLRLVAPTACWPEEKLVEQCRALAQKNGGNITLTEDIAAGVKGADFIYTDVWVSMGEA 240

Query: 241 KEKWAERIALLRGYQVNAQMMALTDNPNVKFLHCLPAFHDDQTTLGKQMAKEFDLHGGME 300
           KEKWAERIALLR YQVN++MMALT NP VKFLHCLPAFHDDQTTLGKQMA E+ LHGGME
Sbjct: 241 KEKWAERIALLRAYQVNSEMMALTGNPQVKFLHCLPAFHDDQTTLGKQMAAEYGLHGGME 300

Query: 301 VTDEVFESAASIVFDQAENRMHTIKAVMMATLGE 334
           VTDEVFESAASIVFDQAENRMHTIKAVM+ATLG+
Sbjct: 301 VTDEVFESAASIVFDQAENRMHTIKAVMVATLGK 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: 486
Number of extensions: 12
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 BWI76_RS03010 BWI76_RS03010 (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.15893.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                               -----------
   7.1e-140  451.4   0.0     8e-140  451.2   0.0    1.0  1  lcl|FitnessBrowser__Koxy:BWI76_RS03010  BWI76_RS03010 ornithine carbamoy


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Koxy:BWI76_RS03010  BWI76_RS03010 ornithine carbamoyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  451.2   0.0    8e-140    8e-140       1     303 [.       7     332 ..       7     333 .. 0.99

  Alignments for each domain:
  == domain 1  score: 451.2 bits;  conditional E-value: 8e-140
                               TIGR00658   1 rhllslldlseeelkellelakklkkekkkgkeekklkgktlaliFekrstRtRvsfevaayelGaqvlyl 71 
                                             +h+l+lld++++e++ llela++lk++kk++ e ++l+gk++aliFek+stRtR+sfevaa+++Ga+v+yl
  lcl|FitnessBrowser__Koxy:BWI76_RS03010   7 KHFLKLLDFTPAEITALLELAARLKADKKNNIEIQHLTGKNIALIFEKDSTRTRCSFEVAAFDQGARVTYL 77 
                                             79********************************************************************* PP

                               TIGR00658  72 nkeelqlgrkesikDtarvlsryvdaivvRvykhedveelakyasvPvingLtdlehPcqilaDlltikek 142
                                             +++ +q+g+kesikDtarvl+r++d+i++R++ +e ve+la+ya+vPv+ngLt+++hP+q+laDllt++e+
  lcl|FitnessBrowser__Koxy:BWI76_RS03010  78 GPSGSQIGHKESIKDTARVLGRMYDGIQYRGHGQEVVETLAEYAGVPVWNGLTNEFHPTQLLADLLTMQEH 148
                                             *********************************************************************** PP

                               TIGR00658 143 lg..klkevklvyvGDa.nnvanslllaaaklGldvvvatPeglepeaeivkkakkiakenggkleltedp 210
                                             l   ++++++lvy GDa nn++ns+l aaa++Gld+++++P +++pe+++v++++++a++ngg+++lted+
  lcl|FitnessBrowser__Koxy:BWI76_RS03010 149 LPgkAFNQMTLVYAGDArNNMGNSMLEAAALTGLDLRLVAPTACWPEEKLVEQCRALAQKNGGNITLTEDI 219
                                             *8889****************************************************************** PP

                               TIGR00658 211 kkavkdadviytDvwvsmGe.eekkeerlkllkpyqvneellela.kpevkflhCLPavr........... 268
                                             + +vk+ad+iytDvwvsmGe +ek++er++ll+ yqvn+e+++l+ +p+vkflhCLPa++           
  lcl|FitnessBrowser__Koxy:BWI76_RS03010 220 AAGVKGADFIYTDVWVSMGEaKEKWAERIALLRAYQVNSEMMALTgNPQVKFLHCLPAFHddqttlgkqma 290
                                             ********************9999*********************************************** PP

                               TIGR00658 269 .......GeevtdevlegeasivfdeaenRlhaqkavlkall 303
                                                    G+evtdev+e++asivfd+aenR+h++kav++a+l
  lcl|FitnessBrowser__Koxy:BWI76_RS03010 291 aeyglhgGMEVTDEVFESAASIVFDQAENRMHTIKAVMVATL 332
                                             ***************************************998 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 10.31
//
[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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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, 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