Alignments for a candidate for arcB in Dinoroseobacter shibae DFL-12

GapMind for catabolism of small carbon sources

Alignments for a candidate for arcB in Dinoroseobacter shibae DFL-12

Align ornithine carbamoyltransferase (EC 2.1.3.3) (characterized)
to candidate 3607382 Dshi_0796 ornithine carbamoyltransferase (RefSeq)

Query= BRENDA::Q98BB6
         (303 letters)



>FitnessBrowser__Dino:3607382
          Length = 308

 Score =  356 bits (913), Expect = e-103
 Identities = 179/305 (58%), Positives = 219/305 (71%), Gaps = 7/305 (2%)

Query: 5   HFTDLSTVSEGDLRFMLDDA----VVRKARLK-AGERTRPLEGKVLAMIFDKPSTRTRVS 59
           HF D+ T    DLR MLD        R  R K A +  +PL G ++A+IF+KPSTRTRVS
Sbjct: 3   HFLDIHTTDPADLRAMLDRGRAMKTARAGRPKGASDDDQPLAGHMVALIFEKPSTRTRVS 62

Query: 60  FDVGMRQLGGETIMLTGTEMQLGRSETIADTAKVLSRYVDAIMIRTTSHDRLLELTENAT 119
           FD+G+RQ+GG+T++L+G +MQLG  ETIADTA+VLSRYVD IMIRT     LLE+ E+A+
Sbjct: 63  FDLGVRQMGGQTMVLSGADMQLGHGETIADTARVLSRYVDLIMIRTFEETTLLEMAEHAS 122

Query: 120 VPVINGLTDDTHPCQLMADIMTFEEHRGPVAGKTIAWTGDGNNVLHSLLEASARFRFNLN 179
           VPVINGLT+ THPCQ+MAD+MT+EEHRGP+AGK + W GDGNNV  S L A+ +F F++ 
Sbjct: 123 VPVINGLTNRTHPCQIMADVMTYEEHRGPIAGKKVVWCGDGNNVCASFLHAAGQFGFDMT 182

Query: 180 VAVPEGSEPAQKHIDWSKAHGGKLHFTRSPEEAVDQADCVVTDCWVSM--GQEHRARGHN 237
              P   +P  + +  ++A G  +   R P  AV  AD VV D WVSM   Q  + R HN
Sbjct: 183 FTGPPTLDPEAEFVAGARAKGVTVEIERDPAVAVQGADLVVADTWVSMHDSQTTKERRHN 242

Query: 238 VFSPYQVNAKLMAHAKPDALFMHCLPAHRGEEVTDEVIDGPHSVVFDEAENRLHAQKAVL 297
              PYQV+  LM  AKPDALFMHCLPAHRGEEVT EV+DGPHSV+FDEAENRLHAQKAV+
Sbjct: 243 QLRPYQVDRALMEKAKPDALFMHCLPAHRGEEVTSEVMDGPHSVIFDEAENRLHAQKAVM 302

Query: 298 AWCLG 302
            WCLG
Sbjct: 303 RWCLG 307


Lambda     K      H
   0.320    0.133    0.400 

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: 340
Number of extensions: 14
Number of successful extensions: 3
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: 303
Length of database: 308
Length adjustment: 27
Effective length of query: 276
Effective length of database: 281
Effective search space:    77556
Effective search space used:    77556
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 (21.8 bits)
S2: 48 (23.1 bits)

Align candidate 3607382 Dshi_0796 (ornithine carbamoyltransferase (RefSeq))
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.15022.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
     2e-116  374.4   0.0   2.3e-116  374.2   0.0    1.0  1  lcl|FitnessBrowser__Dino:3607382  Dshi_0796 ornithine carbamoyltra


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dino:3607382  Dshi_0796 ornithine carbamoyltransferase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  374.2   0.0  2.3e-116  2.3e-116       2     303 ..       3     306 ..       2     307 .. 0.96

  Alignments for each domain:
  == domain 1  score: 374.2 bits;  conditional E-value: 2.3e-116
                         TIGR00658   2 hllslldlseeelkellelakklkkekkkgke.....ekklkgktlaliFekrstRtRvsfevaayelGaqvlylnk 73 
                                       h+l+++  ++++l+ +l++++ +k+++    +     ++ l g+ +aliFek+stRtRvsf+ ++ ++G+q+++l+ 
  lcl|FitnessBrowser__Dino:3607382   3 HFLDIHTTDPADLRAMLDRGRAMKTARAGRPKgasddDQPLAGHMVALIFEKPSTRTRVSFDLGVRQMGGQTMVLSG 79 
                                       9***********************9887544445566999************************************* PP

                         TIGR00658  74 eelqlgrkesikDtarvlsryvdaivvRvykhedveelakyasvPvingLtdlehPcqilaDlltikeklgklkevk 150
                                        ++qlg++e+i+Dtarvlsryvd i++R+++++++ e+a++asvPvingLt+ +hPcqi+aD++t +e+ g + + k
  lcl|FitnessBrowser__Dino:3607382  80 ADMQLGHGETIADTARVLSRYVDLIMIRTFEETTLLEMAEHASVPVINGLTNRTHPCQIMADVMTYEEHRGPIAGKK 156
                                       ***************************************************************************** PP

                         TIGR00658 151 lvyvGDannvanslllaaaklGldvvvatPeglepeaeivkkakkiakenggkleltedpkkavkdadviytDvwvs 227
                                       +v+ GD+nnv+ s+l aa ++G+d++ ++P+ l+peae v  a+    ++g ++e+ +dp+ av++ad+++ D+wvs
  lcl|FitnessBrowser__Dino:3607382 157 VVWCGDGNNVCASFLHAAGQFGFDMTFTGPPTLDPEAEFVAGAR----AKGVTVEIERDPAVAVQGADLVVADTWVS 229
                                       ****************************************9995....59*************************** PP

                         TIGR00658 228 mGe.eekkeerlkllkpyqvneellelakpevkflhCLPavrGeevtdevlegeasivfdeaenRlhaqkavlkall 303
                                       m + +++ke r ++l+pyqv++ l+e akp++ f+hCLPa+rGeevt ev++g++s++fdeaenRlhaqkav+ ++l
  lcl|FitnessBrowser__Dino:3607382 230 MHDsQTTKERRHNQLRPYQVDRALMEKAKPDALFMHCLPAHRGEEVTSEVMDGPHSVIFDEAENRLHAQKAVMRWCL 306
                                       **95667777889************************************************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (304 nodes)
Target sequences:                          1  (308 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 6.82
//
[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 (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