GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argI 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.aa/TIGR00658.hmm
# target sequence database:        /tmp/gapView.29105.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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 7.78
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

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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