Alignments for a candidate for arcB in Phaeobacter inhibens BS107

GapMind for catabolism of small carbon sources

Alignments for a candidate for arcB in Phaeobacter inhibens BS107

Align ornithine carbamoyltransferase (EC 2.1.3.3) (characterized)
to candidate GFF2391 PGA1_c24220 ornithine carbamoyltransferase ArgF

Query= BRENDA::Q98BB6
         (303 letters)



>FitnessBrowser__Phaeo:GFF2391
          Length = 308

 Score =  343 bits (879), Expect = 4e-99
 Identities = 174/308 (56%), Positives = 221/308 (71%), Gaps = 7/308 (2%)

Query: 3   VRHFTDLSTVSEGDLRFMLDDA-VVRKARL----KAGERTRPLEGKVLAMIFDKPSTRTR 57
           + HF D+      DLR ++D A   ++ARL     A +   PL+ +++A+IF+KPSTRTR
Sbjct: 1   MNHFLDIHKTDATDLRAIIDQASATKQARLGRPKAAPDDELPLKDRMVALIFEKPSTRTR 60

Query: 58  VSFDVGMRQLGGETIMLTGTEMQLGRSETIADTAKVLSRYVDAIMIRTTSHDRLLELTEN 117
           VSFDVG+RQ+GG+T++L+G +MQLG  ETIADTA+VLSRYVD IMIRT     L E+ E 
Sbjct: 61  VSFDVGVRQMGGQTMVLSGNDMQLGHGETIADTARVLSRYVDMIMIRTFDETVLTEMAEY 120

Query: 118 ATVPVINGLTDDTHPCQLMADIMTFEEHRGPVAGKTIAWTGDGNNVLHSLLEASARFRFN 177
           A+VPVINGLTD THPCQ+MAD++T+EEHRGP+ GK + W GDGNNV  S L A+A+F F+
Sbjct: 121 ASVPVINGLTDRTHPCQIMADVLTYEEHRGPIKGKKVVWCGDGNNVCASFLHAAAQFGFD 180

Query: 178 LNVAVPEGSEPAQKHIDWSKAHGGKLHFTRSPEEAVDQADCVVTDCWVSM--GQEHRARG 235
           L    P   +P  + I  ++  G ++   R   +AV+ AD VV D WVSM   Q  + R 
Sbjct: 181 LTFTGPAQLDPEPEFIGLARNAGSQVIIERDAAKAVEGADLVVADTWVSMHDSQSSKERR 240

Query: 236 HNVFSPYQVNAKLMAHAKPDALFMHCLPAHRGEEVTDEVIDGPHSVVFDEAENRLHAQKA 295
           HN+   YQVN  LMAHAKPDALFMHCLPAHR EEVT  V+DGP SV+FDEAENRLHAQKA
Sbjct: 241 HNMLRGYQVNDALMAHAKPDALFMHCLPAHREEEVTSAVMDGPQSVIFDEAENRLHAQKA 300

Query: 296 VLAWCLGA 303
           ++ +CLGA
Sbjct: 301 IMRYCLGA 308


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: 333
Number of extensions: 7
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 GFF2391 PGA1_c24220 (ornithine carbamoyltransferase ArgF)
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.4461.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
   7.8e-116  372.5   0.0   8.8e-116  372.3   0.0    1.0  1  lcl|FitnessBrowser__Phaeo:GFF2391  PGA1_c24220 ornithine carbamoylt


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Phaeo:GFF2391  PGA1_c24220 ornithine carbamoyltransferase ArgF
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  372.3   0.0  8.8e-116  8.8e-116       2     303 ..       3     306 ..       2     307 .. 0.96

  Alignments for each domain:
  == domain 1  score: 372.3 bits;  conditional E-value: 8.8e-116
                          TIGR00658   2 hllslldlseeelkellelakklkkekkkgke.....ekklkgktlaliFekrstRtRvsfevaayelGaqvlyln 72 
                                        h+l++++ +  +l+ ++++a+  k+++    +     e  lk + +aliFek+stRtRvsf+v++ ++G+q+++l+
  lcl|FitnessBrowser__Phaeo:GFF2391   3 HFLDIHKTDATDLRAIIDQASATKQARLGRPKaapddELPLKDRMVALIFEKPSTRTRVSFDVGVRQMGGQTMVLS 78 
                                        9***********************9876543345555899************************************ PP

                          TIGR00658  73 keelqlgrkesikDtarvlsryvdaivvRvykhedveelakyasvPvingLtdlehPcqilaDlltikeklgklke 148
                                         +++qlg++e+i+Dtarvlsryvd+i++R+++++ ++e+a+yasvPvingLtd +hPcqi+aD+lt +e+ g +k+
  lcl|FitnessBrowser__Phaeo:GFF2391  79 GNDMQLGHGETIADTARVLSRYVDMIMIRTFDETVLTEMAEYASVPVINGLTDRTHPCQIMADVLTYEEHRGPIKG 154
                                        **************************************************************************** PP

                          TIGR00658 149 vklvyvGDannvanslllaaaklGldvvvatPeglepeaeivkkakkiakenggkleltedpkkavkdadviytDv 224
                                         k+v+ GD+nnv+ s+l aaa++G+d++ ++P +l+pe+e +  a    ++ g+++ + +d +kav++ad+++ D+
  lcl|FitnessBrowser__Phaeo:GFF2391 155 KKVVWCGDGNNVCASFLHAAAQFGFDLTFTGPAQLDPEPEFIGLA----RNAGSQVIIERDAAKAVEGADLVVADT 226
                                        ******************************************988....569************************ PP

                          TIGR00658 225 wvsmGe.eekkeerlkllkpyqvneellelakpevkflhCLPavrGeevtdevlegeasivfdeaenRlhaqkavl 299
                                        wvsm + +++ke r ++l++yqvn+ l+++akp++ f+hCLPa+r eevt  v++g++s++fdeaenRlhaqka++
  lcl|FitnessBrowser__Phaeo:GFF2391 227 WVSMHDsQSSKERRHNMLRGYQVNDALMAHAKPDALFMHCLPAHREEEVTSAVMDGPQSVIFDEAENRLHAQKAIM 302
                                        *****95667777889************************************************************ PP

                          TIGR00658 300 kall 303
                                         ++l
  lcl|FitnessBrowser__Phaeo:GFF2391 303 RYCL 306
                                        9876 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 11.36
//
[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