Alignments for a candidate for hutG' in Azospirillum brasilense Sp245

GapMind for catabolism of small carbon sources

Alignments for a candidate for hutG' in Azospirillum brasilense Sp245

Align N-formylglutamate deformylase (EC 3.5.1.68) (characterized)
to candidate AZOBR_RS08115 AZOBR_RS08115 N-formylglutamate amidohydrolase

Query= reanno::acidovorax_3H11:Ac3H11_2548
         (270 letters)



>FitnessBrowser__azobra:AZOBR_RS08115
          Length = 275

 Score =  268 bits (685), Expect = 9e-77
 Identities = 137/268 (51%), Positives = 173/268 (64%), Gaps = 5/268 (1%)

Query: 8   FTFHQGTAPLLVSMPHAGTYVPPVLAARFTDEARQVPDTDWHMERLYAFAKDMGASILVA 67
           F F  G  P+L+S+PH GT VPP +AA  TD A  +PDTDWH++RLY FA  +G   L  
Sbjct: 4   FRFQPGETPVLLSIPHVGTVVPPDIAATMTDSALAMPDTDWHLDRLYHFAPALGIGFLKP 63

Query: 68  THSRYVVDLNRPPDGASLYPG-QSVTGLCPVDTFDDTPIYAQGDVPDDAEVAARRDAVWA 126
             SRYV+DLNR PD     PG  S T LCP+ TFD  P+Y  G  PD  EV  R  A W 
Sbjct: 64  ILSRYVIDLNRDPDSDLPIPGGASSTELCPLTTFDHQPVYRPGQEPDAVEVRRRIGAYWR 123

Query: 127 PYHAQLRAELSRIRAQHGVAVLWDAHSIRSVLPRFFEGKLPDLNLGTADGASCDPALAQA 186
           PYH QL  EL  ++ + GVAVL+DAHSIRS +PRFF+G++ D +LGTA+G S  PAL   
Sbjct: 124 PYHEQLNGELQALKERFGVAVLFDAHSIRSRVPRFFDGQIQDFSLGTAEGTSASPALVGR 183

Query: 187 LLAIAQSAPGYTGVLNGRFKGGHITRHYGQPAQNIHAVQLEMTQCSYMQEALPFDYLPEV 246
           ++ +  +   ++ V NGRFKGG ITR YG PA NIH++QLE++Q +YM E  PF +  E 
Sbjct: 184 VMNVLTATGRFSSVQNGRFKGGFITRRYGNPADNIHSIQLELSQLTYMDEEAPFGFREES 243

Query: 247 AAEVQPHLERLL----EAALAFAAARRK 270
           A +V+P LERLL    E A   AA RR+
Sbjct: 244 ARQVRPTLERLLSLVVEWAWENAAGRRR 271


Lambda     K      H
   0.321    0.135    0.416 

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: 236
Number of extensions: 7
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: 270
Length of database: 275
Length adjustment: 25
Effective length of query: 245
Effective length of database: 250
Effective search space:    61250
Effective search space used:    61250
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: 47 (22.7 bits)

Align candidate AZOBR_RS08115 AZOBR_RS08115 (N-formylglutamate amidohydrolase)
to HMM TIGR02017 (hutG: N-formylglutamate deformylase (EC 3.5.1.68))

# 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/TIGR02017.hmm
# target sequence database:        /tmp/gapView.4122.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR02017  [M=263]
Accession:   TIGR02017
Description: hutG_amidohyd: N-formylglutamate deformylase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    2.7e-96  308.0   0.0    3.2e-96  307.8   0.0    1.0  1  lcl|FitnessBrowser__azobra:AZOBR_RS08115  AZOBR_RS08115 N-formylglutamate 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__azobra:AZOBR_RS08115  AZOBR_RS08115 N-formylglutamate amidohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  307.8   0.0   3.2e-96   3.2e-96       3     261 ..       4     262 ..       2     264 .. 0.97

  Alignments for each domain:
  == domain 1  score: 307.8 bits;  conditional E-value: 3.2e-96
                                 TIGR02017   3 levqrGkaPllislPhtGtdltdavesrlvsaakalkdtdWhieklydfardlGatvvraaisrlvidv 71 
                                               +++q G++P+l+s+Ph Gt +++++++ ++++a+a+ dtdWh+++ly fa  lG  +++  +sr+vid+
  lcl|FitnessBrowser__azobra:AZOBR_RS08115   4 FRFQPGETPVLLSIPHVGTVVPPDIAATMTDSALAMPDTDWHLDRLYHFAPALGIGFLKPILSRYVIDL 72 
                                               67999**************************************************************** PP

                                 TIGR02017  72 nrdps.gaslypgqattgliPettfdgeplykdGeaPseaeikkrltkyfkPyhaalraeierlralhg 139
                                               nrdp+ + ++  g + t+l+P ttfd +p+y+ G++P++ e+++r+  y++Pyh++l+ e++ l++ +g
  lcl|FitnessBrowser__azobra:AZOBR_RS08115  73 NRDPDsDLPIPGGASSTELCPLTTFDHQPVYRPGQEPDAVEVRRRIGAYWRPYHEQLNGELQALKERFG 141
                                               **98636788889999***************************************************** PP

                                 TIGR02017 140 kivlydahsirsviPrlfeGklPdfnlGtndgkscdpaladaveavcakakglssvlnGrfkGGyitrh 208
                                               ++vl+dahsirs++Pr+f+G++ df lGt +g s+ pal  +v++v++ +  +ssv nGrfkGG+itr 
  lcl|FitnessBrowser__azobra:AZOBR_RS08115 142 VAVLFDAHSIRSRVPRFFDGQIQDFSLGTAEGTSASPALVGRVMNVLTATGRFSSVQNGRFKGGFITRR 210
                                               ************************************************77789**************** PP

                                 TIGR02017 209 ygqPqngvhavqlelaqrgyleeetePvaydeakaealravlkellealldfa 261
                                               yg+P++++h++qlel+q +y++ e  P+ ++e+ a+++r +l++ll+ ++++a
  lcl|FitnessBrowser__azobra:AZOBR_RS08115 211 YGNPADNIHSIQLELSQLTYMD-EEAPFGFREESARQVRPTLERLLSLVVEWA 262
                                               **********************.889**************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (263 nodes)
Target sequences:                          1  (275 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: 00:00:00.00
# Mc/sec: 10.88
//
[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