Alignments for a candidate for hutF in Pseudomonas putida KT2440

GapMind for catabolism of small carbon sources

Alignments for a candidate for hutF in Pseudomonas putida KT2440

Align formiminoglutamate deiminase subunit (EC 3.5.3.13) (characterized)
to candidate PP_5036 PP_5036 probable formiminoglutamate deiminase

Query= metacyc::MONOMER-11614
         (454 letters)



>FitnessBrowser__Putida:PP_5036
          Length = 454

 Score =  789 bits (2037), Expect = 0.0
 Identities = 385/453 (84%), Positives = 412/453 (90%)

Query: 1   MSAFFAERALLPDGWANHVRLEVSANGQLTQIQANASADGAERLKGPLLPGMPNLHSHAF 60
           MSA+FAERALLP GWA+HVR+EV+++G++  I+  ASA+ AERL GPLLPGMPNLHSHAF
Sbjct: 1   MSAYFAERALLPTGWASHVRIEVASDGRVASIEPGASAEDAERLAGPLLPGMPNLHSHAF 60

Query: 61  QRAMAGLAEVAGNPNDSFWTWRDLMYRLVGKINPEQLEVIARQLYIEMLKAGYTSVAEFH 120
           QRAMAGLAEVAGNPNDSFWTWRDLMYRLVG+I+PEQL+VIARQLYIEMLKAGYTSVAEFH
Sbjct: 61  QRAMAGLAEVAGNPNDSFWTWRDLMYRLVGQISPEQLQVIARQLYIEMLKAGYTSVAEFH 120

Query: 121 YVHHDSDGKPYADPAELSRRISQAAAGSGIGLTLLPVLYSHAGFGGQAPNDGQRRFINST 180
           YVHHD  GKPYADPAELSRRIS AAA SGIGLTLLPVLYSHAGFGGQAPNDGQRRFINST
Sbjct: 121 YVHHDQAGKPYADPAELSRRISAAAADSGIGLTLLPVLYSHAGFGGQAPNDGQRRFINST 180

Query: 181 ENYLKLQQHLQPLLAQQANQQLGLCFHSLRAVTPQQISEVLAASDRHCPVHIHIAEQQKE 240
           E YL+LQ  L PLLA Q  Q LGLCFHSLRAV P QI+EVLAASDR CPVHIHIAEQQKE
Sbjct: 181 EQYLQLQAQLFPLLAAQPAQHLGLCFHSLRAVRPGQIAEVLAASDRQCPVHIHIAEQQKE 240

Query: 241 VDDCLSWSGRRPLQWLYENVAVDQRWCLVHATHANPEEVSLMARSRAIAGLCLTTEANLG 300
           VDDCL+WSG RPLQWLYE+V VD+RWCLVHATHA P+EV+ MARS A+AGLCLTTEANLG
Sbjct: 241 VDDCLAWSGLRPLQWLYEHVDVDRRWCLVHATHAEPDEVTAMARSGAVAGLCLTTEANLG 300

Query: 301 DGIFPAVDFLAQGGRLGIGSDSHVSLSVVEELRWLEYGQRLRDQRRNRLYRADQPMVGRT 360
           DGIFPAVDFLAQGGR+GIGSDSHVSLSVVEELRWLEYGQRLRDQRRNRLYR DQPMVGRT
Sbjct: 301 DGIFPAVDFLAQGGRMGIGSDSHVSLSVVEELRWLEYGQRLRDQRRNRLYRGDQPMVGRT 360

Query: 361 LYDAALDGGAQALGQGIGALAVGTRADWLVLDGNDPYLATADGDGILNRWLFAGGDRQVR 420
           LYDAAL GGAQALGQ IG LAVG RADWLVLDG DPY+A A+GD ILNRWLFAGGDRQVR
Sbjct: 361 LYDAALSGGAQALGQAIGELAVGKRADWLVLDGQDPYIAMAEGDAILNRWLFAGGDRQVR 420

Query: 421 DVMVGGQWVVRDGRHAAEEDSSRAFTQVLRDLL 453
           DVMV GQWVVR GRHA E++S RAF +VLR LL
Sbjct: 421 DVMVNGQWVVRQGRHAQEDESGRAFAKVLRQLL 453


Lambda     K      H
   0.320    0.135    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: 787
Number of extensions: 17
Number of successful extensions: 1
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: 454
Length of database: 454
Length adjustment: 33
Effective length of query: 421
Effective length of database: 421
Effective search space:   177241
Effective search space used:   177241
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: 51 (24.3 bits)

Align candidate PP_5036 PP_5036 (probable formiminoglutamate 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.9312.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
     2e-237  774.2   2.1   2.2e-237  774.0   2.1    1.0  1  lcl|FitnessBrowser__Putida:PP_5036  PP_5036 probable formiminoglutam


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Putida:PP_5036  PP_5036 probable formiminoglutamate deiminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  774.0   2.1  2.2e-237  2.2e-237       1     454 [.       1     453 [.       1     454 [] 1.00

  Alignments for each domain:
  == domain 1  score: 774.0 bits;  conditional E-value: 2.2e-237
                           TIGR02022   1 akvyfaerallpdgwaegvrlavaedGrilavetgvsaaedaerlsgvvlpglanlHsHAFqralaGlaevagsg 75 
                                         +++yfaerallp+gwa++vr++va+dGr++++e g+s aedaerl+g++lpg++nlHsHAFqra+aGlaevag++
  lcl|FitnessBrowser__Putida:PP_5036   1 MSAYFAERALLPTGWASHVRIEVASDGRVASIEPGAS-AEDAERLAGPLLPGMPNLHSHAFQRAMAGLAEVAGNP 74 
                                         578**********************************.************************************* PP

                           TIGR02022  76 aDsFWtWRevmYrlverldPeqleaiarqlyvemlkaGftrvgEFHYlHHaadGtpYadpaelaeriaaAAadaG 150
                                         +DsFWtWR++mYrlv +++Peql++iarqly+emlkaG+t+v+EFHY+HH+++G+pYadpael++ri+aAAad+G
  lcl|FitnessBrowser__Putida:PP_5036  75 NDSFWTWRDLMYRLVGQISPEQLQVIARQLYIEMLKAGYTSVAEFHYVHHDQAGKPYADPAELSRRISAAAADSG 149
                                         *************************************************************************** PP

                           TIGR02022 151 igltlLpvlYahagFGgaaanegqrrfiddveaflrlvealrkelaaqeearlGlaiHslRAvtaeelaavlqas 225
                                         igltlLpvlY+hagFGg+a+n+gqrrfi+++e++l+l+++l + laaq++++lGl++HslRAv++ ++a+vl+as
  lcl|FitnessBrowser__Putida:PP_5036 150 IGLTLLPVLYSHAGFGGQAPNDGQRRFINSTEQYLQLQAQLFPLLAAQPAQHLGLCFHSLRAVRPGQIAEVLAAS 224
                                         *************************************************************************** PP

                           TIGR02022 226 erqlPvHiHvaEqqkEvddClaasgrrPvewLldhaevdarwclvHatHltdeevkllaksgavaglCpttEanL 300
                                         +rq+PvHiH+aEqqkEvddCla+sg rP++wL++h++vd+rwclvHatH +++ev+++a+sgavaglC+ttEanL
  lcl|FitnessBrowser__Putida:PP_5036 225 DRQCPVHIHIAEQQKEVDDCLAWSGLRPLQWLYEHVDVDRRWCLVHATHAEPDEVTAMARSGAVAGLCLTTEANL 299
                                         *************************************************************************** PP

                           TIGR02022 301 gDGifpaadfvaaggrlgiGsDshvvvdvleElRllEygqRLrdraRnvlaageeasvaralydaAlaggaqalG 375
                                         gDGifpa+df+a+ggr+giGsDshv+++v+eElR+lEygqRLrd++Rn+l++g++++v+r+lydaAl+ggaqalG
  lcl|FitnessBrowser__Putida:PP_5036 300 GDGIFPAVDFLAQGGRMGIGSDSHVSLSVVEELRWLEYGQRLRDQRRNRLYRGDQPMVGRTLYDAALSGGAQALG 374
                                         *************************************************************************** PP

                           TIGR02022 376 laegeleaGarADlltldledpslagakgdalldsllfaaekaavrdvvvaGrkvvrdgrHaleeeierafakvl 450
                                         +a gel++G+rAD+l+ld++dp++a+a+gda+l+++lfa+++++vrdv+v+G++vvr+grHa+e+e++rafakvl
  lcl|FitnessBrowser__Putida:PP_5036 375 QAIGELAVGKRADWLVLDGQDPYIAMAEGDAILNRWLFAGGDRQVRDVMVNGQWVVRQGRHAQEDESGRAFAKVL 449
                                         *************************************************************************** PP

                           TIGR02022 451 rall 454
                                         r+ll
  lcl|FitnessBrowser__Putida:PP_5036 450 RQLL 453
                                         *997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (455 nodes)
Target sequences:                          1  (454 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 7.04
//
[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