Alignments for a candidate for arcB in Sulfuritalea hydrogenivorans sk43H DSM 22779

GapMind for catabolism of small carbon sources

Alignments for a candidate for arcB in Sulfuritalea hydrogenivorans sk43H DSM 22779

Align Ornithine carbamoyltransferase (EC 2.1.3.3) (characterized)
to candidate WP_041097709.1 SUTH_RS05535 ornithine carbamoyltransferase

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



>NCBI__GCF_000828635.1:WP_041097709.1
          Length = 307

 Score =  426 bits (1094), Expect = e-124
 Identities = 208/302 (68%), Positives = 249/302 (82%), Gaps = 1/302 (0%)

Query: 2   AIKHYLQFSDFTLDEYEYVIERSRVIKRKFKNYEPHHTLADRTLVMVFEKNSTRTRLSFE 61
           A +H+LQ  D + DE ++V ER+R IK +FK Y+ +  L DRTLVM+FEK STRTRLSFE
Sbjct: 3   APRHFLQLKDLSRDELDHVFERTRSIKARFKAYQRYWPLQDRTLVMIFEKASTRTRLSFE 62

Query: 62  AGMHQMGGAAIYLNTRDSQLGRGEPVEDAAQVMSRMCDVIMIRTYGQEIIERFAKHSRVP 121
           AGM Q+GG+AIYLNTRDSQLGRGEPVEDAAQV+SRM D++MIRT+ QEIIERFA HSRVP
Sbjct: 63  AGMQQLGGSAIYLNTRDSQLGRGEPVEDAAQVISRMSDIVMIRTFEQEIIERFAGHSRVP 122

Query: 122 VINGLTNEQHPCQVLADVFTYIEHHGSIQGKIVAWVGDANNMLYSWLQAAEVFGFHVNVS 181
           VINGLTNE HPCQ+LAD+FT+IE  G IQG+ VAW+GD+NN+  +WLQAAEVF F+V+VS
Sbjct: 123 VINGLTNEYHPCQILADIFTFIEQRGPIQGRTVAWIGDSNNVCNTWLQAAEVFDFNVHVS 182

Query: 182 TPKGYDIDPAQVS-PGNKNYTFFADPADACQDADLVTTDVWTSMGFEAENNARLKAFDGW 240
           TP GY+++P +    G  ++  FADP DA + ADLVTTDVWTSMGFEAEN+ RL+ F  W
Sbjct: 183 TPPGYEVEPERAGLYGTGHFEEFADPMDAARGADLVTTDVWTSMGFEAENDERLRDFADW 242

Query: 241 IVDQAKMARAKKDALFMHCLPAHRGEEVAAEVIDGPQSVVWEEAENRLHVQKALLEYLVH 300
            VD   M  AK +A+FMHCLPAHRGEEVAAEVIDG QSVVW+EAENRLHVQKAL+E+L+ 
Sbjct: 243 QVDADMMHAAKPEAVFMHCLPAHRGEEVAAEVIDGAQSVVWDEAENRLHVQKALMEFLLL 302

Query: 301 GR 302
           GR
Sbjct: 303 GR 304


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: 11
Number of successful extensions: 2
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: 307
Length adjustment: 27
Effective length of query: 277
Effective length of database: 280
Effective search space:    77560
Effective search space used:    77560
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_041097709.1 SUTH_RS05535 (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.2931286.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   6.9e-113  362.8   0.0   8.4e-113  362.5   0.0    1.1  1  NCBI__GCF_000828635.1:WP_041097709.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000828635.1:WP_041097709.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  362.5   0.0  8.4e-113  8.4e-113       1     303 [.       5     301 ..       5     302 .. 0.98

  Alignments for each domain:
  == domain 1  score: 362.5 bits;  conditional E-value: 8.4e-113
                             TIGR00658   1 rhllslldlseeelkellelakklkkekkkgkeekklkgktlaliFekrstRtRvsfevaayelGaqvlylnk 73 
                                           rh+l+l+dls++el ++ e+++++k++ k+ ++   l+ +tl +iFek+stRtR+sfe+++ +lG+ ++yln+
  NCBI__GCF_000828635.1:WP_041097709.1   5 RHFLQLKDLSRDELDHVFERTRSIKARFKAYQRYWPLQDRTLVMIFEKASTRTRLSFEAGMQQLGGSAIYLNT 77 
                                           8************************************************************************ PP

                             TIGR00658  74 eelqlgrkesikDtarvlsryvdaivvRvykhedveelakyasvPvingLtdlehPcqilaDlltikeklgkl 146
                                            ++qlgr+e+++D a+v+sr+ d++++R++++e++e +a ++ vPvingLt++ hPcqilaD++t +e+ g +
  NCBI__GCF_000828635.1:WP_041097709.1  78 RDSQLGRGEPVEDAAQVISRMSDIVMIRTFEQEIIERFAGHSRVPVINGLTNEYHPCQILADIFTFIEQRGPI 150
                                           ************************************************************************* PP

                             TIGR00658 147 kevklvyvGDannvanslllaaaklGldvvvatPeglepeaeivkkakkiakenggkleltedpkkavkdadv 219
                                           ++ +++++GD+nnv+n+ l aa  + ++v+v+tP+g+e e+e             g++e   dp +a+++ad+
  NCBI__GCF_000828635.1:WP_041097709.1 151 QGRTVAWIGDSNNVCNTWLQAAEVFDFNVHVSTPPGYEVEPERAGLY------GTGHFEEFADPMDAARGADL 217
                                           ***************************************99744333......4499**************** PP

                             TIGR00658 220 iytDvwvsmGeeekkeerlkllkpyqvneellelakpevkflhCLPavrGeevtdevlegeasivfdeaenRl 292
                                           + tDvw+smG e++++erl+ + ++qv+ ++++ akpe++f+hCLPa+rGeev+ ev++g++s+v+deaenRl
  NCBI__GCF_000828635.1:WP_041097709.1 218 VTTDVWTSMGFEAENDERLRDFADWQVDADMMHAAKPEAVFMHCLPAHRGEEVAAEVIDGAQSVVWDEAENRL 290
                                           ************************************************************************* PP

                             TIGR00658 293 haqkavlkall 303
                                           h+qka++++ll
  NCBI__GCF_000828635.1:WP_041097709.1 291 HVQKALMEFLL 301
                                           ********987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (304 nodes)
Target sequences:                          1  (307 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 18.51
//
[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:

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 2024 update 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