GapMind for catabolism of small carbon sources

 

Alignments for a candidate for arcB in Lactobacillus silagei IWT126

Align Ornithine carbamoyltransferase, catabolic; OTCase; EC 2.1.3.3 (characterized)
to candidate WP_089137031.1 CES79_RS09540 ornithine carbamoyltransferase

Query= SwissProt::Q8G998
         (343 letters)



>NCBI__GCF_002217945.1:WP_089137031.1
          Length = 342

 Score =  587 bits (1514), Expect = e-172
 Identities = 286/341 (83%), Positives = 312/341 (91%)

Query: 3   KDFRQNVFQGRSVLAEKDFSAAELEYLIDFGLHLKALKKAGIPHHYLEGKNIALLFEKSS 62
           K+F+ +VFQGRSVLAEKDFSAAEL YLIDFGLHLKALKKAG+PHHYLEGKNIALLFEK+S
Sbjct: 2   KEFKNSVFQGRSVLAEKDFSAAELNYLIDFGLHLKALKKAGVPHHYLEGKNIALLFEKNS 61

Query: 63  TRTRSAFTTASIDLGAHPEYLGQNDIQLGKKESTSDTAKVLGSMFDGIEFRGFKQSDAEI 122
           TRTRSAFTTA+IDLGAHPE+LG NDIQLGKKES  DTAKVLGSMFDGIEFRGF Q   E 
Sbjct: 62  TRTRSAFTTAAIDLGAHPEFLGANDIQLGKKESVEDTAKVLGSMFDGIEFRGFSQKVVEQ 121

Query: 123 LARDSGVPVWNGLTDEWHPTQMLADFMTVKENFGKLQGLTLTFMGDGRNNVANSLLVTGA 182
           LA  SGVPVWNGLTDEWHPTQMLADFMTVKENFG L+GLTLT+MGDGRNN+ANSLLVTGA
Sbjct: 122 LAEFSGVPVWNGLTDEWHPTQMLADFMTVKENFGHLKGLTLTYMGDGRNNMANSLLVTGA 181

Query: 183 ILGVNIHIVAPKALFPTEETQNIAKGFAEKSGAKLVITDDLDEGLKGSNVVYTDVWVSMG 242
           ILGVNIHIVAP  L P +E Q++A GFA+ SGAKL+ITDDLDEGLKGSN+VYTDVWVSMG
Sbjct: 182 ILGVNIHIVAPNELHPAQEIQDLANGFAKDSGAKLLITDDLDEGLKGSNIVYTDVWVSMG 241

Query: 243 ESNWEERVKELTPYQVNMEAMKKTGTPDDQLIFMHCLPAFHNTDTQYGKEIKEKYGITEM 302
           E+NW+ER+  L PYQVNM A+KKT TPDDQLI MHCLPAFH+T T YGKEI+EKYG+TEM
Sbjct: 242 ENNWQERINLLKPYQVNMAALKKTDTPDDQLIVMHCLPAFHDTTTDYGKEIQEKYGLTEM 301

Query: 303 EVTDEVFTSKYARQFEEAENRMHSIKAMMAATLGNLFIPRV 343
           E+TDEVF SKYARQFEEAENRMHSIKAMMAATLG+LFIP+V
Sbjct: 302 EITDEVFRSKYARQFEEAENRMHSIKAMMAATLGDLFIPKV 342


Lambda     K      H
   0.317    0.133    0.383 

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: 536
Number of extensions: 16
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: 343
Length of database: 342
Length adjustment: 29
Effective length of query: 314
Effective length of database: 313
Effective search space:    98282
Effective search space used:    98282
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 (21.6 bits)
S2: 49 (23.5 bits)

Align candidate WP_089137031.1 CES79_RS09540 (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.3698508.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   5.3e-119  382.9   0.0     6e-119  382.7   0.0    1.0  1  NCBI__GCF_002217945.1:WP_089137031.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_002217945.1:WP_089137031.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  382.7   0.0    6e-119    6e-119       2     303 ..      13     334 ..      12     335 .. 0.98

  Alignments for each domain:
  == domain 1  score: 382.7 bits;  conditional E-value: 6e-119
                             TIGR00658   2 hllslldlseeelkellelakklkkekkkgkeekklkgktlaliFekrstRtRvsfevaayelGaqvlylnke 74 
                                           ++l+ +d+s +el++l++ + +lk+ kk+g+ +++l+gk++al+Fek+stRtR +f++aa++lGa++ +l+++
  NCBI__GCF_002217945.1:WP_089137031.1  13 SVLAEKDFSAAELNYLIDFGLHLKALKKAGVPHHYLEGKNIALLFEKNSTRTRSAFTTAAIDLGAHPEFLGAN 85 
                                           677889******************************************************************* PP

                             TIGR00658  75 elqlgrkesikDtarvlsryvdaivvRvykhedveelakyasvPvingLtdlehPcqilaDlltikeklgklk 147
                                           ++qlg+kes++Dta+vl++++d+i +R+++++ ve+la++++vPv+ngLtd+ hP+q+laD++t+ke++g+lk
  NCBI__GCF_002217945.1:WP_089137031.1  86 DIQLGKKESVEDTAKVLGSMFDGIEFRGFSQKVVEQLAEFSGVPVWNGLTDEWHPTQMLADFMTVKENFGHLK 158
                                           ************************************************************************* PP

                             TIGR00658 148 evklvyvGDa.nnvanslllaaaklGldvvvatPeglepeaeivkkakkiakenggkleltedpkkavkdadv 219
                                           +++l+y+GD+ nn+ansll+++a lG+++++++P++l+p +ei + a+ +ak++g+kl +t+d ++++k++++
  NCBI__GCF_002217945.1:WP_089137031.1 159 GLTLTYMGDGrNNMANSLLVTGAILGVNIHIVAPNELHPAQEIQDLANGFAKDSGAKLLITDDLDEGLKGSNI 231
                                           ************************************************************************* PP

                             TIGR00658 220 iytDvwvsmGeeekkeerlkllkpyqvneellela...kpevkflhCLPavr.................Geev 272
                                           +ytDvwvsmGe+ +++er++llkpyqvn+  l+ +   +++ +++hCLPa++                  +e+
  NCBI__GCF_002217945.1:WP_089137031.1 232 VYTDVWVSMGEN-NWQERINLLKPYQVNMAALKKTdtpDDQLIVMHCLPAFHdtttdygkeiqekygltEMEI 303
                                           **********75.689****************9986567899************************9999*** PP

                             TIGR00658 273 tdevlegeasivfdeaenRlhaqkavlkall 303
                                           tdev+ ++  + f+eaenR+h++ka+++a+l
  NCBI__GCF_002217945.1:WP_089137031.1 304 TDEVFRSKYARQFEEAENRMHSIKAMMAATL 334
                                           ****************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (304 nodes)
Target sequences:                          1  (342 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: 13.53
//
[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