Alignments for a candidate for hutG' in Caulobacter crescentus NA1000

GapMind for catabolism of small carbon sources

Alignments for a candidate for hutG' in Caulobacter crescentus NA1000

Align N-formylglutamate deformylase (EC 3.5.1.68) (characterized)
to candidate CCNA_01009 CCNA_01009 N-formylglutamate deformylase

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



>FitnessBrowser__Caulo:CCNA_01009
          Length = 271

 Score =  335 bits (859), Expect = 6e-97
 Identities = 168/265 (63%), Positives = 199/265 (75%), Gaps = 7/265 (2%)

Query: 2   IHVEQGSAPLIVSVPHAGTVIPADIQG-LVSPELARYDADLYVDHLYAFARGLDATIVRT 60
           + V +GSAPLI+S+PH GT IP DI+  L SP LAR DAD +V+ LYAFA  L AT+VRT
Sbjct: 5   LQVVRGSAPLIISLPHTGTDIPPDIESQLASPWLARKDADWWVEQLYAFAENLGATLVRT 64

Query: 61  TVSRTVIDVNRDPSGQTLYPGQFTTGLCPIQTFDGTPLYEPGALPDAHEIERRRAEWFDP 120
            +SRTVIDVNRDPSG +LYPGQ TT LCP  TFDG PLY  G  PDA EI+ RR  +F+P
Sbjct: 65  AISRTVIDVNRDPSGASLYPGQATTELCPTTTFDGEPLYRDGG-PDAAEIDHRRTTYFEP 123

Query: 121 YHTALAIQIERLRAIHPAIVVYDAHSIRSVVPKLFDGELPNFNIGTNDGTSCAPALTQAV 180
           YH AL  +IERLRA+HP +V+Y+AHSIRS VP+LF+GELP FN+GTN G SCA ALT AV
Sbjct: 124 YHAALRSEIERLRAVHPTVVLYEAHSIRSRVPRLFEGELPQFNLGTNSGQSCADALTVAV 183

Query: 181 EAICDASPYSRVTNGRFKGGWITRHYARPAGGVHSIQMELAMRTYLVE-----TPAHWPP 235
           EA CDAS  SRVTNGRFKGGW TRHY +PA GVH+IQMELA R Y+ +     TP  WP 
Sbjct: 184 EAACDASGLSRVTNGRFKGGWTTRHYGQPATGVHAIQMELACRGYMDDPAEPPTPDTWPT 243

Query: 236 PWHEETAQACQSVLRPILSAAIDFA 260
           P+H   A+  ++VL  +L A +DFA
Sbjct: 244 PFHAARAEPLRAVLEEVLGACLDFA 268


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: 282
Number of extensions: 9
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: 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 CCNA_01009 CCNA_01009 (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.18981.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   5.4e-140  451.3   0.0   6.1e-140  451.1   0.0    1.0  1  lcl|FitnessBrowser__Caulo:CCNA_01009  CCNA_01009 N-formylglutamate def


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Caulo:CCNA_01009  CCNA_01009 N-formylglutamate deformylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  451.1   0.0  6.1e-140  6.1e-140       1     262 [.       3     269 ..       3     270 .. 0.99

  Alignments for each domain:
  == domain 1  score: 451.1 bits;  conditional E-value: 6.1e-140
                             TIGR02017   1 dalevqrGkaPllislPhtGtdltdavesrlvsaakalkdtdWhieklydfardlGatvvraaisrlvidvnr 73 
                                           d+l+v rG+aPl+islPhtGtd+++++es+l+s+++a+kd+dW++e+ly+fa++lGat+vr+aisr+vidvnr
  lcl|FitnessBrowser__Caulo:CCNA_01009   3 DWLQVVRGSAPLIISLPHTGTDIPPDIESQLASPWLARKDADWWVEQLYAFAENLGATLVRTAISRTVIDVNR 75 
                                           79*********************************************************************** PP

                             TIGR02017  74 dpsgaslypgqattgliPettfdgeplykdGeaPseaeikkrltkyfkPyhaalraeierlralhgkivlyda 146
                                           dpsgaslypgqatt+l+P+ttfdgeply+dG  P++aei++r+t+yf+Pyhaalr+eierlra+h+++vly+a
  lcl|FitnessBrowser__Caulo:CCNA_01009  76 DPSGASLYPGQATTELCPTTTFDGEPLYRDG-GPDAAEIDHRRTTYFEPYHAALRSEIERLRAVHPTVVLYEA 147
                                           *******************************.9**************************************** PP

                             TIGR02017 147 hsirsviPrlfeGklPdfnlGtndgkscdpaladaveavcakakglssvlnGrfkGGyitrhygqPqngvhav 219
                                           hsirs++PrlfeG+lP+fnlGtn+g+sc++al+ avea+c+ a+gls+v+nGrfkGG++trhygqP++gvha+
  lcl|FitnessBrowser__Caulo:CCNA_01009 148 HSIRSRVPRLFEGELPQFNLGTNSGQSCADALTVAVEAACD-ASGLSRVTNGRFKGGWTTRHYGQPATGVHAI 219
                                           *****************************************.******************************* PP

                             TIGR02017 220 qlelaqrgylee.......etePvaydeakaealravlkellealldfae 262
                                           q+ela+rgy+++       +t+P+++++a+ae+lravl+e+l a+ldfa+
  lcl|FitnessBrowser__Caulo:CCNA_01009 220 QMELACRGYMDDpaepptpDTWPTPFHAARAEPLRAVLEEVLGACLDFAN 269
                                           ************************************************98 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 7.90
//
[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