Alignments for a candidate for hutG' in Stenotrophomonas chelatiphaga DSM 21508

GapMind for catabolism of small carbon sources

Alignments for a candidate for hutG' in Stenotrophomonas chelatiphaga DSM 21508

Align N-formylglutamate deformylase (EC 3.5.1.68) (characterized)
to candidate WP_057506765.1 ABB28_RS00615 N-formylglutamate deformylase

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



>NCBI__GCF_001431535.1:WP_057506765.1
          Length = 284

 Score =  294 bits (753), Expect = 1e-84
 Identities = 153/271 (56%), Positives = 184/271 (67%), Gaps = 12/271 (4%)

Query: 2   IHVEQGSAPLIVSVPHAGTVIPADIQG-LVSPELARYDADLYVDHLYAFARGLDATIVRT 60
           + V +G APL++S PH GT +P D+ G  VSP LAR DAD +V  LYAFARGL AT VR+
Sbjct: 8   LEVHEGDAPLLISFPHTGTALPDDLAGRFVSPWLARRDADWWVHELYAFARGLGATTVRS 67

Query: 61  TVSRTVIDVNRDPSGQTLYPGQFTTGLCPIQTFDGTPLYEPGALPDAHEIERRRAEWFDP 120
           ++SR+VID+NRDPSG +LYPGQ TTGLCP+ TFD  PLY+P   PD  EI RRR  +F P
Sbjct: 68  SISRSVIDLNRDPSGVSLYPGQNTTGLCPLTTFDNQPLYKPAQEPDEAEILRRREAYFAP 127

Query: 121 YHTALAIQIERLRAIHPAIVVYDAHSIRSVVPKLFDGELPNFNIGT-----NDGTSCAPA 175
           YH ALA QI RLRA H  +VVYDAHSIRS +P LFDGELP FN+GT        TSC  A
Sbjct: 128 YHAALASQIARLRARHGTVVVYDAHSIRSRIPHLFDGELPQFNLGTAGPTGEVDTSCDNA 187

Query: 176 LTQAVEAICDASPYSRVTNGRFKGGWITRHYARPAGGVHSIQMELAMRTYLVETPAH--- 232
           L+  VE +C  S    V NGRFKGGWITRHY+   GGVHS+QMELA R Y+ E  A    
Sbjct: 188 LSDVVENLCRLSGLPHVRNGRFKGGWITRHYSDIPGGVHSLQMELACRGYMAEPAAEALD 247

Query: 233 ---WPPPWHEETAQACQSVLRPILSAAIDFA 260
              WP P  ++ A   +  L  +L+A ++FA
Sbjct: 248 AHSWPTPLDDDHATPLRHTLAQVLTACLEFA 278


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: 284
Number of extensions: 16
Number of successful extensions: 4
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: 284
Length adjustment: 25
Effective length of query: 239
Effective length of database: 259
Effective search space:    61901
Effective search space used:    61901
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_057506765.1 ABB28_RS00615 (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.30674.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   5.7e-120  385.6   0.0   6.6e-120  385.4   0.0    1.0  1  lcl|NCBI__GCF_001431535.1:WP_057506765.1  ABB28_RS00615 N-formylglutamate 


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_001431535.1:WP_057506765.1  ABB28_RS00615 N-formylglutamate deformylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  385.4   0.0  6.6e-120  6.6e-120       2     262 ..       7     279 ..       6     280 .. 0.97

  Alignments for each domain:
  == domain 1  score: 385.4 bits;  conditional E-value: 6.6e-120
                                 TIGR02017   2 alevqrGkaPllislPhtGtdltdavesrlvsaakalkdtdWhieklydfardlGatvvraaisrlvid 70 
                                               +lev++G+aPllis+PhtGt l+d+++ r+vs+++a++d+dW++++ly+far lGat+vr++isr+vid
  lcl|NCBI__GCF_001431535.1:WP_057506765.1   7 WLEVHEGDAPLLISFPHTGTALPDDLAGRFVSPWLARRDADWWVHELYAFARGLGATTVRSSISRSVID 75 
                                               99******************************************************************* PP

                                 TIGR02017  71 vnrdpsgaslypgqattgliPettfdgeplykdGeaPseaeikkrltkyfkPyhaalraeierlralhg 139
                                               +nrdpsg+slypgq+ttgl+P ttfd++plyk  ++P+eaei +r++ yf Pyhaal+++i+rlra hg
  lcl|NCBI__GCF_001431535.1:WP_057506765.1  76 LNRDPSGVSLYPGQNTTGLCPLTTFDNQPLYKPAQEPDEAEILRRREAYFAPYHAALASQIARLRARHG 144
                                               ********************************************************************* PP

                                 TIGR02017 140 kivlydahsirsviPrlfeGklPdfnlGt.....ndgkscdpaladaveavcakakglssvlnGrfkGG 203
                                               ++v+ydahsirs+iP+lf+G+lP+fnlGt     + + scd+al+d ve++c+  +gl +v+nGrfkGG
  lcl|NCBI__GCF_001431535.1:WP_057506765.1 145 TVVVYDAHSIRSRIPHLFDGELPQFNLGTagptgEVDTSCDNALSDVVENLCR-LSGLPHVRNGRFKGG 212
                                               ****************************9444334689**************9.*************** PP

                                 TIGR02017 204 yitrhygqPqngvhavqlelaqrgylee........etePvaydeakaealravlkellealldfae 262
                                               +itrhy++   gvh++q+ela+rgy++e         ++P++ d+++a++lr +l ++l+a+l+fa+
  lcl|NCBI__GCF_001431535.1:WP_057506765.1 213 WITRHYSDIPGGVHSLQMELACRGYMAEpaaealdaHSWPTPLDDDHATPLRHTLAQVLTACLEFAS 279
                                               **********************************9999***************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (263 nodes)
Target sequences:                          1  (284 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 11.11
//
[ok]

This GapMind analysis is from Sep 24 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