Alignments for a candidate for hutF in Caulobacter crescentus NA1000

GapMind for catabolism of small carbon sources

Alignments for a candidate for hutF in Caulobacter crescentus NA1000

Align formimidoylglutamate deiminase (EC 3.5.3.13) (characterized)
to candidate CCNA_01012 CCNA_01012 N-formimino-L-glutamate deiminase

Query= BRENDA::Q9HU77
         (453 letters)



>FitnessBrowser__Caulo:CCNA_01012
          Length = 459

 Score =  429 bits (1104), Expect = e-125
 Identities = 231/454 (50%), Positives = 296/454 (65%), Gaps = 10/454 (2%)

Query: 2   SAIFAERALLPEGWARNVRFEISADGVLAEIRPDANADGAERLGGAVLPGMPNLHSHAFQ 61
           + ++ E ALL +GWAR V+F I ADG +A I  DA A  A RLG A LPG+ N+HSHAFQ
Sbjct: 12  TVVWCESALLADGWARGVKFTI-ADGRIARIDTDAPAGDALRLGPA-LPGLGNVHSHAFQ 69

Query: 62  RAMAGLAEVAGNPNDSFWTWRELMYRMVARLSPEQIEVIACQLYIEMLKAGYTAVAEFHY 121
           RAMAGLAE  G   D+FWTWRE+MYR +ARL P+  + IA    +EML+ G+T V EFHY
Sbjct: 70  RAMAGLAETRGETGDNFWTWREVMYRFLARLDPDMAQAIAAMGQVEMLEGGFTRVGEFHY 129

Query: 122 VHHDLDGRSYADPAELSLRISRAASAAGIGLTLLPVLYSHAGFGGQPASEGQRRFINGSE 181
           +HH  DG  Y +PAE++ R++ AA   GIGLTLLPV Y+H+ FGG P ++GQ+RFI+  +
Sbjct: 130 LHHAPDGGFYDNPAEMAARMAAAADETGIGLTLLPVFYAHSNFGGLPPTDGQKRFIHDVD 189

Query: 182 AYLELLQRLRAPLEAAGHSL-GLCFHSLRAVTPQQIATVL--AAGHDDLPVHIHIAEQQK 238
            +  L++  R  +     ++ G+  HSLRAVT +++  +L  AAG    PVH+H+AEQ K
Sbjct: 190 GFARLVEACRGIVAGLPEAVVGIAPHSLRAVTGEELDAILPLAAGG---PVHMHVAEQTK 246

Query: 239 EVDDCQAWSGRRPLQWLYENVAVDQRWCLVHATHADPAEVAAMARSGAVAGLCLSTEANL 298
           EVDDC A +G+RP++WL  +  VDQRWCL+HATH +  E   +A+SGAVAGLC  TEANL
Sbjct: 247 EVDDCLAATGQRPVRWLMNHTEVDQRWCLIHATHINATETERLAKSGAVAGLCPVTEANL 306

Query: 299 GDGIFPATDFLAQGGRLGIGSDSHVSLSVVEELRWLEYGQRLRDRKRNRLYRDDQPMIGR 358
           GDGIFP  D+LA GGR GIG+DS++ +   +ELR LEY QRL  R RN L    +   G 
Sbjct: 307 GDGIFPTPDYLAAGGRFGIGTDSNIVIDAAQELRTLEYAQRLSRRARNVLASGPRRATGG 366

Query: 359 TLYDAALAGGAQALGQPIGSLAVGRRADLLVLDGNDPYLASAEGDALLNRWLFAGGDRQV 418
            L+ AA  GGAQALG   G L  G  AD L LD N P L    GD L++  +FAGG   +
Sbjct: 367 DLWRAAALGGAQALGAGRGELRRGAPADFLTLDPNHPNLVGRTGDTLIDSLVFAGGG--I 424

Query: 419 RDVMVAGRWVVRDGRHAGEERSARAFVQVLGELL 452
             V   GR +V  GRH   E     +VQ L  LL
Sbjct: 425 DTVWRQGRQLVSGGRHHAREAITTRYVQTLQALL 458


Lambda     K      H
   0.321    0.136    0.415 

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: 616
Number of extensions: 27
Number of successful extensions: 6
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: 453
Length of database: 459
Length adjustment: 33
Effective length of query: 420
Effective length of database: 426
Effective search space:   178920
Effective search space used:   178920
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: 51 (24.3 bits)

Align candidate CCNA_01012 CCNA_01012 (N-formimino-L-glutamate deiminase)
to HMM TIGR02022 (hutF: formiminoglutamate deiminase (EC 3.5.3.13))

# 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/TIGR02022.hmm
# target sequence database:        /tmp/gapView.678453.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR02022  [M=455]
Accession:   TIGR02022
Description: hutF: formiminoglutamate deiminase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   3.5e-220  717.4   1.2   3.9e-220  717.2   1.2    1.0  1  FitnessBrowser__Caulo:CCNA_01012  


Domain annotation for each sequence (and alignments):
>> FitnessBrowser__Caulo:CCNA_01012  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  717.2   1.2  3.9e-220  3.9e-220       2     455 .]      12     459 .]      11     459 .] 0.99

  Alignments for each domain:
  == domain 1  score: 717.2 bits;  conditional E-value: 3.9e-220
                         TIGR02022   2 kvyfaerallpdgwaegvrlavaedGrilavetgvsaaedaerlsgvvlpglanlHsHAFqralaGlaevagsgaDs 78 
                                       +v+++e+all+dgwa+gv++++a dGri++++t+++ a da rl+ ++lpgl+n+HsHAFqra+aGlae++g+++D+
  FitnessBrowser__Caulo:CCNA_01012  12 TVVWCESALLADGWARGVKFTIA-DGRIARIDTDAP-AGDALRLG-PALPGLGNVHSHAFQRAMAGLAETRGETGDN 85 
                                       799*******************9.88**********.88888887.******************************* PP

                         TIGR02022  79 FWtWRevmYrlverldPeqleaiarqlyvemlkaGftrvgEFHYlHHaadGtpYadpaelaeriaaAAadaGigltl 155
                                       FWtWRevmYr+++rldP++++aia++ +veml++GftrvgEFHYlHHa+dG +Y++pae+a+r+aaAA+++Gigltl
  FitnessBrowser__Caulo:CCNA_01012  86 FWTWREVMYRFLARLDPDMAQAIAAMGQVEMLEGGFTRVGEFHYLHHAPDGGFYDNPAEMAARMAAAADETGIGLTL 162
                                       ***************************************************************************** PP

                         TIGR02022 156 LpvlYahagFGgaaanegqrrfiddveaflrlvealrkelaaqeearlGlaiHslRAvtaeelaavlqaserqlPvH 232
                                       Lpv+Yah++FGg ++++gq+rfi+dv+ f+rlvea+r  +a+ +ea++G+a+HslRAvt eel+a+l++++   PvH
  FitnessBrowser__Caulo:CCNA_01012 163 LPVFYAHSNFGGLPPTDGQKRFIHDVDGFARLVEACRGIVAGLPEAVVGIAPHSLRAVTGEELDAILPLAAGG-PVH 238
                                       **********************************************************************996.*** PP

                         TIGR02022 233 iHvaEqqkEvddClaasgrrPvewLldhaevdarwclvHatHltdeevkllaksgavaglCpttEanLgDGifpaad 309
                                       +HvaEq+kEvddClaa+g+rPv+wL++h+evd+rwcl+HatH++++e+++laksgavaglCp+tEanLgDGifp+ d
  FitnessBrowser__Caulo:CCNA_01012 239 MHVAEQTKEVDDCLAATGQRPVRWLMNHTEVDQRWCLIHATHINATETERLAKSGAVAGLCPVTEANLGDGIFPTPD 315
                                       ***************************************************************************** PP

                         TIGR02022 310 fvaaggrlgiGsDshvvvdvleElRllEygqRLrdraRnvlaageeasvaralydaAlaggaqalGlaegeleaGar 386
                                       ++aaggr+giG+Ds++v+d+++ElR+lEy+qRL++raRnvla+g++++++ +l++aA++ggaqalG+ +gel++Ga+
  FitnessBrowser__Caulo:CCNA_01012 316 YLAAGGRFGIGTDSNIVIDAAQELRTLEYAQRLSRRARNVLASGPRRATGGDLWRAAALGGAQALGAGRGELRRGAP 392
                                       ***************************************************************************** PP

                         TIGR02022 387 ADlltldledpslagakgdalldsllfaaekaavrdvvvaGrkvvrdgrHaleeeierafakvlralla 455
                                       AD+ltld ++p+l+g++gd+l+dsl+fa+++  +++v+++Gr+ v++grH+++e+i+++++++l+alla
  FitnessBrowser__Caulo:CCNA_01012 393 ADFLTLDPNHPNLVGRTGDTLIDSLVFAGGG--IDTVWRQGRQLVSGGRHHAREAITTRYVQTLQALLA 459
                                       *****************************76..*********************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (455 nodes)
Target sequences:                          1  (459 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: 22.57
//
[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