Alignments for a candidate for arcB in Azoarcus sp. BH72

GapMind for catabolism of small carbon sources

Alignments for a candidate for arcB in Azoarcus sp. BH72

Align Ornithine carbamoyltransferase (EC 2.1.3.3) (characterized)
to candidate WP_011765918.1 AZO_RS11055 ornithine carbamoyltransferase

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



>NCBI__GCF_000061505.1:WP_011765918.1
          Length = 311

 Score =  454 bits (1168), Expect = e-132
 Identities = 219/300 (73%), Positives = 253/300 (84%), Gaps = 1/300 (0%)

Query: 4   KHYLQFSDFTLDEYEYVIERSRVIKRKFKNYEPHHTLADRTLVMVFEKNSTRTRLSFEAG 63
           +HYLQFSDFT  EY++V +R+R IK KFK YEP+H L DRTLVM+FEK STRTRLSFEAG
Sbjct: 5   RHYLQFSDFTAAEYDHVFQRTRWIKEKFKQYEPYHPLFDRTLVMIFEKASTRTRLSFEAG 64

Query: 64  MHQMGGAAIYLNTRDSQLGRGEPVEDAAQVMSRMCDVIMIRTYGQEIIERFAKHSRVPVI 123
           M Q+GG+AIYLNTRDSQLGRGEPVEDAAQV+SRM D++MIRT+ Q+IIERFA +SRVPVI
Sbjct: 65  MQQLGGSAIYLNTRDSQLGRGEPVEDAAQVISRMSDLVMIRTFEQDIIERFAAYSRVPVI 124

Query: 124 NGLTNEQHPCQVLADVFTYIEHHGSIQGKIVAWVGDANNMLYSWLQAAEVFGFHVNVSTP 183
           NGLTNE HPCQ+LAD++T+IEH GSI+GK VAWVGD+NNM  +WLQAAEV  F V VSTP
Sbjct: 125 NGLTNEYHPCQILADIYTFIEHRGSIKGKTVAWVGDSNNMCNTWLQAAEVLDFKVRVSTP 184

Query: 184 KGYDIDPAQVS-PGNKNYTFFADPADACQDADLVTTDVWTSMGFEAENNARLKAFDGWIV 242
            GY+++P      G  ++  F+DP +AC+ ADLVTTDVWTSMGFEAEN AR+KAF  W V
Sbjct: 185 PGYEVEPTDAGLRGTAHFAQFSDPLEACRGADLVTTDVWTSMGFEAENEARMKAFADWCV 244

Query: 243 DQAKMARAKKDALFMHCLPAHRGEEVAAEVIDGPQSVVWEEAENRLHVQKALLEYLVHGR 302
           D   M+ A  DALFMHCLPAHRGEEV AEVIDGPQSVVW+EAENRLHVQKAL+EYLV GR
Sbjct: 245 DAEMMSVAAPDALFMHCLPAHRGEEVTAEVIDGPQSVVWDEAENRLHVQKALMEYLVLGR 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: 374
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: 311
Length adjustment: 27
Effective length of query: 277
Effective length of database: 284
Effective search space:    78668
Effective search space used:    78668
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_011765918.1 AZO_RS11055 (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.19999.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   6.6e-111  356.3   0.0   8.2e-111  356.0   0.0    1.1  1  lcl|NCBI__GCF_000061505.1:WP_011765918.1  AZO_RS11055 ornithine carbamoylt


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000061505.1:WP_011765918.1  AZO_RS11055 ornithine carbamoyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  356.0   0.0  8.2e-111  8.2e-111       1     303 [.       5     301 ..       5     302 .. 0.97

  Alignments for each domain:
  == domain 1  score: 356.0 bits;  conditional E-value: 8.2e-111
                                 TIGR00658   1 rhllslldlseeelkellelakklkkekkkgkeekklkgktlaliFekrstRtRvsfevaayelGaqvl 69 
                                               rh+l++ d++ +e  ++ ++++ +k++ k+ +  + l  +tl +iFek+stRtR+sfe+++ +lG+ ++
  lcl|NCBI__GCF_000061505.1:WP_011765918.1   5 RHYLQFSDFTAAEYDHVFQRTRWIKEKFKQYEPYHPLFDRTLVMIFEKASTRTRLSFEAGMQQLGGSAI 73 
                                               79****************************999************************************ PP

                                 TIGR00658  70 ylnkeelqlgrkesikDtarvlsryvdaivvRvykhedveelakyasvPvingLtdlehPcqilaDllt 138
                                               yln+ ++qlgr+e+++D a+v+sr+ d +++R+++++++e +a y+ vPvingLt++ hPcqilaD+ t
  lcl|NCBI__GCF_000061505.1:WP_011765918.1  74 YLNTRDSQLGRGEPVEDAAQVISRMSDLVMIRTFEQDIIERFAAYSRVPVINGLTNEYHPCQILADIYT 142
                                               ********************************************************************* PP

                                 TIGR00658 139 ikeklgklkevklvyvGDannvanslllaaaklGldvvvatPeglepeaeivkkakkiakenggklelt 207
                                                +e+ g++k+ ++++vGD+nn++n+ l aa  l ++v+v+tP+g+e e++    a     +  +++   
  lcl|NCBI__GCF_000061505.1:WP_011765918.1 143 FIEHRGSIKGKTVAWVGDSNNMCNTWLQAAEVLDFKVRVSTPPGYEVEPTD---A---GLRGTAHFAQF 205
                                               **********************************************98753...2...33566899999 PP

                                 TIGR00658 208 edpkkavkdadviytDvwvsmGeeekkeerlkllkpyqvneellelakpevkflhCLPavrGeevtdev 276
                                               +dp +a ++ad++ tDvw+smG e+++e+r+k++ ++ v+ e++++a p++ f+hCLPa+rGeevt ev
  lcl|NCBI__GCF_000061505.1:WP_011765918.1 206 SDPLEACRGADLVTTDVWTSMGFEAENEARMKAFADWCVDAEMMSVAAPDALFMHCLPAHRGEEVTAEV 274
                                               ********************************************************************* PP

                                 TIGR00658 277 legeasivfdeaenRlhaqkavlkall 303
                                               ++g++s+v+deaenRlh+qka++++l+
  lcl|NCBI__GCF_000061505.1:WP_011765918.1 275 IDGPQSVVWDEAENRLHVQKALMEYLV 301
                                               ***********************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (304 nodes)
Target sequences:                          1  (311 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: 10.63
//
[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:

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