Alignments for a candidate for hutG' in Methylobacterium nodulans ORS 2060

GapMind for catabolism of small carbon sources

Alignments for a candidate for hutG' in Methylobacterium nodulans ORS 2060

Align N-formylglutamate deformylase (EC 3.5.1.68) (characterized)
to candidate WP_015927743.1 MNOD_RS04995 N-formylglutamate deformylase

Query= reanno::Korea:Ga0059261_3962
         (264 letters)



>NCBI__GCF_000022085.1:WP_015927743.1
          Length = 271

 Score =  293 bits (751), Expect = 2e-84
 Identities = 152/266 (57%), Positives = 183/266 (68%), Gaps = 9/266 (3%)

Query: 4   VEQGSAPLIVSVPHAGTVIPADIQG-LVSPELARYDADLYVDHLYAFARGLDATIVRTTV 62
           V QG+APLI+S+PH GT IP +I+  LVSP LAR D D +++ LY FA GLDATI+RT +
Sbjct: 8   VRQGTAPLILSLPHTGTEIPPEIEAALVSPWLARKDTDWWIERLYDFAAGLDATIIRTAL 67

Query: 63  SRTVIDVNRDPSGQTLYPGQFTTGLCPIQTFDGTPLYEPGALPDAHEIERRRAEWFDPYH 122
           SRTVIDVNRDPSG +LYPGQ TT LCP  TFDG PLY  G  PD  E   RR  WFDPYH
Sbjct: 68  SRTVIDVNRDPSGVSLYPGQATTELCPTTTFDGEPLYREGEGPDVAE---RRTRWFDPYH 124

Query: 123 TALAIQIERLRAIHPAIVVYDAHSIRSVVPKLFDGELPNFNIGTNDGTSCAPALTQAVEA 182
            AL  +I RLR +HP IV+YD HSIRS +P+LF G LP+FNIGT+ G +C PAL   +E 
Sbjct: 125 AALQGEIARLRRLHPRIVLYDCHSIRSEIPRLFPGLLPHFNIGTDGGRTCDPALQDEIER 184

Query: 183 ICDASPYSRVTNGRFKGGWITRHYARPAGGVHSIQMELAMRTYLVET-----PAHWPPPW 237
           IC A+  S V+NGRF+GG+ITR Y  PA GVH++QMELA R YL E      P  WP P+
Sbjct: 185 ICAATGLSVVSNGRFRGGFITRAYGCPADGVHAVQMELACRAYLDEPVGPVGPETWPVPY 244

Query: 238 HEETAQACQSVLRPILSAAIDFAKAP 263
               A   ++ L  IL+A + F   P
Sbjct: 245 DPVRAAPVRTALESILAACLAFGARP 270


Lambda     K      H
   0.321    0.136    0.426 

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: 305
Number of extensions: 9
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: 264
Length of database: 271
Length adjustment: 25
Effective length of query: 239
Effective length of database: 246
Effective search space:    58794
Effective search space used:    58794
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: 47 (22.7 bits)

Align candidate WP_015927743.1 MNOD_RS04995 (N-formylglutamate deformylase)
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.1237398.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   3.3e-126  406.1   0.0   3.7e-126  405.9   0.0    1.0  1  NCBI__GCF_000022085.1:WP_015927743.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000022085.1:WP_015927743.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  405.9   0.0  3.7e-126  3.7e-126       2     262 ..       5     268 ..       4     269 .. 0.99

  Alignments for each domain:
  == domain 1  score: 405.9 bits;  conditional E-value: 3.7e-126
                             TIGR02017   2 alevqrGkaPllislPhtGtdltdavesrlvsaakalkdtdWhieklydfardlGatvvraaisrlvidvnrd 74 
                                           +l+v++G+aPl++slPhtGt++++++e+ lvs+++a+kdtdW+ie+lydfa  l at++r+a+sr+vidvnrd
  NCBI__GCF_000022085.1:WP_015927743.1   5 WLTVRQGTAPLILSLPHTGTEIPPEIEAALVSPWLARKDTDWWIERLYDFAAGLDATIIRTALSRTVIDVNRD 77 
                                           99*********************************************************************** PP

                             TIGR02017  75 psgaslypgqattgliPettfdgeplykdGeaPseaeikkrltkyfkPyhaalraeierlralhgkivlydah 147
                                           psg+slypgqatt+l+P+ttfdgeply++Ge P+ ae   r+t++f+Pyhaal+ ei+rlr lh++ivlyd+h
  NCBI__GCF_000022085.1:WP_015927743.1  78 PSGVSLYPGQATTELCPTTTFDGEPLYREGEGPDVAE---RRTRWFDPYHAALQGEIARLRRLHPRIVLYDCH 147
                                           ********************************98765...7899***************************** PP

                             TIGR02017 148 sirsviPrlfeGklPdfnlGtndgkscdpaladaveavcakakglssvlnGrfkGGyitrhygqPqngvhavq 220
                                           sirs iPrlf G lP+fn+Gt+ g++cdpal+d++e +ca a+gls v nGrf+GG+itr yg P++gvhavq
  NCBI__GCF_000022085.1:WP_015927743.1 148 SIRSEIPRLFPGLLPHFNIGTDGGRTCDPALQDEIERICA-ATGLSVVSNGRFRGGFITRAYGCPADGVHAVQ 219
                                           ****************************************.******************************** PP

                             TIGR02017 221 lelaqrgylee.......etePvaydeakaealravlkellealldfae 262
                                           +ela+r+yl+e       et+Pv+yd+++a+++r+ l+++l a+l+f++
  NCBI__GCF_000022085.1:WP_015927743.1 220 MELACRAYLDEpvgpvgpETWPVPYDPVRAAPVRTALESILAACLAFGA 268
                                           **********************************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (263 nodes)
Target sequences:                          1  (271 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: 19.75
//
[ok]

This GapMind analysis is from Apr 09 2024. 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 2024 update 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