GapMind for catabolism of small carbon sources

 

Alignments for a candidate for arcB in Hydrogenophaga taeniospiralis CCUG 15921 NBRC 102512

Align Ornithine carbamoyltransferase (EC 2.1.3.3) (characterized)
to candidate WP_068174008.1 HTA01S_RS17420 ornithine carbamoyltransferase

Query= reanno::HerbieS:HSERO_RS07185
         (304 letters)



>NCBI__GCF_001592305.1:WP_068174008.1
          Length = 315

 Score =  406 bits (1044), Expect = e-118
 Identities = 200/315 (63%), Positives = 242/315 (76%), Gaps = 11/315 (3%)

Query: 1   MAIKHYLQFSDFTLDEYEYVIERSRVIKRKFKNYEPHHTLAD--RTLVMVFEKNSTRTRL 58
           M I+HYLQF D + DEY Y++ R+  IK KFK  E H   AD  RTL M+FEK STRTR+
Sbjct: 1   MNIRHYLQFKDLSADEYAYLLTRAAFIKAKFKAVEKHQPFADPDRTLAMIFEKASTRTRV 60

Query: 59  SFEAGMHQMGGAAIYLNTRDSQLGRGEPVEDAAQVMSRMCDVIMIRTYGQEIIERFAKHS 118
           SFEAGM+Q+GG+ ++L T DSQLGR EP+ED+A+V+SRM D++MIRT+ Q  IERFA HS
Sbjct: 61  SFEAGMYQLGGSVVHLTTGDSQLGRAEPIEDSAKVISRMVDLVMIRTFEQSKIERFAAHS 120

Query: 119 RVPVINGLTNEQHPCQVLADVFTYIEHH--------GSIQGKIVAWVGDANNMLYSWLQA 170
           RVPVINGLTNE HPCQ+LAD+FT +E+          +++GK+V WVGD NNM  +WLQA
Sbjct: 121 RVPVINGLTNEFHPCQILADLFTMVEYRPAASGNPLDALKGKVVTWVGDGNNMANTWLQA 180

Query: 171 AEVFGFHVNVSTPKGYDIDPAQVSPGNKN-YTFFADPADACQDADLVTTDVWTSMGFEAE 229
           AE+ GF V+VSTP GY++DP      N   Y  F DP +AC+ ADLVTTDVWTSMG+EAE
Sbjct: 181 AELLGFTVHVSTPSGYEVDPKLAGVSNPACYKVFKDPKEACKGADLVTTDVWTSMGYEAE 240

Query: 230 NNARLKAFDGWIVDQAKMARAKKDALFMHCLPAHRGEEVAAEVIDGPQSVVWEEAENRLH 289
           N  R  AF  W VD+A MA AK DALFMHCLPAHRGEEV+AEVIDGPQSVVW+EAENR+H
Sbjct: 241 NEVRRAAFAQWCVDEAMMAVAKPDALFMHCLPAHRGEEVSAEVIDGPQSVVWDEAENRMH 300

Query: 290 VQKALLEYLVHGRFD 304
           VQKAL+EYL+ GR +
Sbjct: 301 VQKALMEYLLLGRLN 315


Lambda     K      H
   0.321    0.135    0.409 

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: 347
Number of extensions: 10
Number of successful extensions: 4
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: 304
Length of database: 315
Length adjustment: 27
Effective length of query: 277
Effective length of database: 288
Effective search space:    79776
Effective search space used:    79776
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 48 (23.1 bits)

Align candidate WP_068174008.1 HTA01S_RS17420 (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.1814055.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
     1e-111  358.9   0.0   1.2e-111  358.7   0.0    1.0  1  NCBI__GCF_001592305.1:WP_068174008.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001592305.1:WP_068174008.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  358.7   0.0  1.2e-111  1.2e-111       1     303 [.       4     310 ..       4     311 .. 0.94

  Alignments for each domain:
  == domain 1  score: 358.7 bits;  conditional E-value: 1.2e-111
                             TIGR00658   1 rhllslldlseeelkellelakklkkekkkgkeekklk..gktlaliFekrstRtRvsfevaayelGaqvlyl 71 
                                           rh+l+++dls +e  +ll +a+ +k++ k+ ++++ +    +tla+iFek+stRtRvsfe+++y+lG+ v++l
  NCBI__GCF_001592305.1:WP_068174008.1   4 RHYLQFKDLSADEYAYLLTRAAFIKAKFKAVEKHQPFAdpDRTLAMIFEKASTRTRVSFEAGMYQLGGSVVHL 76 
                                           89****************************999**9973469******************************* PP

                             TIGR00658  72 nkeelqlgrkesikDtarvlsryvdaivvRvykhedveelakyasvPvingLtdlehPcqilaDlltikeklg 144
                                            + ++qlgr e+i+D a+v+sr+vd +++R+++++++e +a ++ vPvingLt+++hPcqilaDl+t+ e+  
  NCBI__GCF_001592305.1:WP_068174008.1  77 TTGDSQLGRAEPIEDSAKVISRMVDLVMIRTFEQSKIERFAAHSRVPVINGLTNEFHPCQILADLFTMVEYRP 149
                                           **********************************************************************975 PP

                             TIGR00658 145 klkev........klvyvGDannvanslllaaaklGldvvvatPeglepeaeivkkakkiakenggklelted 209
                                           + ++          +++vGD+nn+an+ l aa +lG++v+v+tP g+e ++++   +      n +  ++ +d
  NCBI__GCF_001592305.1:WP_068174008.1 150 AASGNpldalkgkVVTWVGDGNNMANTWLQAAELLGFTVHVSTPSGYEVDPKLAGVS------NPACYKVFKD 216
                                           3322222333554799************************************98776......568999**** PP

                             TIGR00658 210 pkkavkdadviytDvwvsmGeeekkeerlkllkpyqvneellelakpevkflhCLPavrGeevtdevlegeas 282
                                           pk+a k+ad++ tDvw+smG e+++e r +++ ++ v+e ++++akp++ f+hCLPa+rGeev+ ev++g++s
  NCBI__GCF_001592305.1:WP_068174008.1 217 PKEACKGADLVTTDVWTSMGYEAENEVRRAAFAQWCVDEAMMAVAKPDALFMHCLPAHRGEEVSAEVIDGPQS 289
                                           ************************************************************************* PP

                             TIGR00658 283 ivfdeaenRlhaqkavlkall 303
                                           +v+deaenR+h+qka++++ll
  NCBI__GCF_001592305.1:WP_068174008.1 290 VVWDEAENRMHVQKALMEYLL 310
                                           *****************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (304 nodes)
Target sequences:                          1  (315 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: 18.63
//
[ok]

This GapMind analysis is from Apr 09 2024. 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