Alignments for a candidate for hutF in Pseudomonas simiae WCS417

GapMind for catabolism of small carbon sources

Alignments for a candidate for hutF in Pseudomonas simiae WCS417

Align Formiminoglutamic iminohydrolase (EC 3.5.3.13) (characterized)
to candidate GFF335 PS417_01705 N-formimino-L-glutamate deiminase

Query= reanno::WCS417:GFF335
         (454 letters)



>FitnessBrowser__WCS417:GFF335
          Length = 454

 Score =  920 bits (2379), Expect = 0.0
 Identities = 454/454 (100%), Positives = 454/454 (100%)

Query: 1   MSAFFAERALLPNGWANDVRLEVSADGLLIKVEANARAEGAERLRGPVLAGMPNLHSHAF 60
           MSAFFAERALLPNGWANDVRLEVSADGLLIKVEANARAEGAERLRGPVLAGMPNLHSHAF
Sbjct: 1   MSAFFAERALLPNGWANDVRLEVSADGLLIKVEANARAEGAERLRGPVLAGMPNLHSHAF 60

Query: 61  QRAMAGLAEVAGNPNDSFWTWRDLMYRMVGKINPDQLQVIARQLYIEMLKAGYTSVAEFH 120
           QRAMAGLAEVAGNPNDSFWTWRDLMYRMVGKINPDQLQVIARQLYIEMLKAGYTSVAEFH
Sbjct: 61  QRAMAGLAEVAGNPNDSFWTWRDLMYRMVGKINPDQLQVIARQLYIEMLKAGYTSVAEFH 120

Query: 121 YVHHDISGQPYADRTELSRQISQAAARSGIGLTLVPVLYTHSGFGGQAPNEGQRRFINST 180
           YVHHDISGQPYADRTELSRQISQAAARSGIGLTLVPVLYTHSGFGGQAPNEGQRRFINST
Sbjct: 121 YVHHDISGQPYADRTELSRQISQAAARSGIGLTLVPVLYTHSGFGGQAPNEGQRRFINST 180

Query: 181 EHYLDLQAQLKPILAAQPAQQLGLCFHSLRAVTPEQINAVLAASDKACPVHIHIAEQQKE 240
           EHYLDLQAQLKPILAAQPAQQLGLCFHSLRAVTPEQINAVLAASDKACPVHIHIAEQQKE
Sbjct: 181 EHYLDLQAQLKPILAAQPAQQLGLCFHSLRAVTPEQINAVLAASDKACPVHIHIAEQQKE 240

Query: 241 VDDCLAWSGKRPLQWLYDNVEVDERWCLVHATHADADEVARMAKSRAIAGLCLTTEANLG 300
           VDDCLAWSGKRPLQWLYDNVEVDERWCLVHATHADADEVARMAKSRAIAGLCLTTEANLG
Sbjct: 241 VDDCLAWSGKRPLQWLYDNVEVDERWCLVHATHADADEVARMAKSRAIAGLCLTTEANLG 300

Query: 301 DGIFPAVDFLAQGGRMGIGSDSHVSLSVVEELRWLEYGQRLRDQRRNRLYRGDQPMVGRT 360
           DGIFPAVDFLAQGGRMGIGSDSHVSLSVVEELRWLEYGQRLRDQRRNRLYRGDQPMVGRT
Sbjct: 301 DGIFPAVDFLAQGGRMGIGSDSHVSLSVVEELRWLEYGQRLRDQRRNRLYRGDQPMVGRT 360

Query: 361 LFDAALDGGAQALGQPIGRLEVGKRADWIVLDGNDPYLATATEDGILNRWLFAGGDRQVR 420
           LFDAALDGGAQALGQPIGRLEVGKRADWIVLDGNDPYLATATEDGILNRWLFAGGDRQVR
Sbjct: 361 LFDAALDGGAQALGQPIGRLEVGKRADWIVLDGNDPYLATATEDGILNRWLFAGGDRQVR 420

Query: 421 DVLVNGKWVVRDGHHAGEEDSNRAFTQVLKDLLD 454
           DVLVNGKWVVRDGHHAGEEDSNRAFTQVLKDLLD
Sbjct: 421 DVLVNGKWVVRDGHHAGEEDSNRAFTQVLKDLLD 454


Lambda     K      H
   0.320    0.136    0.416 

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: 862
Number of extensions: 14
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 GFF335 PS417_01705 (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.22868.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
   4.9e-228  743.2   1.1   5.5e-228  743.1   1.1    1.0  1  lcl|FitnessBrowser__WCS417:GFF335  PS417_01705 N-formimino-L-glutam


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__WCS417:GFF335  PS417_01705 N-formimino-L-glutamate deiminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  743.1   1.1  5.5e-228  5.5e-228       1     454 [.       1     453 [.       1     454 [] 0.99

  Alignments for each domain:
  == domain 1  score: 743.1 bits;  conditional E-value: 5.5e-228
                          TIGR02022   1 akvyfaerallpdgwaegvrlavaedGrilavetgvsaaedaerlsgvvlpglanlHsHAFqralaGlaevagsga 76 
                                        ++++faerallp+gwa++vrl+v++dG + +ve+++  ae+aerl+g+vl+g++nlHsHAFqra+aGlaevag+++
  lcl|FitnessBrowser__WCS417:GFF335   1 MSAFFAERALLPNGWANDVRLEVSADGLLIKVEANAR-AEGAERLRGPVLAGMPNLHSHAFQRAMAGLAEVAGNPN 75 
                                        5789****************************98888.************************************** PP

                          TIGR02022  77 DsFWtWRevmYrlverldPeqleaiarqlyvemlkaGftrvgEFHYlHHaadGtpYadpaelaeriaaAAadaGig 152
                                        DsFWtWR++mYr+v +++P+ql++iarqly+emlkaG+t+v+EFHY+HH+ +G+pYad++el+++i++AAa +Gig
  lcl|FitnessBrowser__WCS417:GFF335  76 DSFWTWRDLMYRMVGKINPDQLQVIARQLYIEMLKAGYTSVAEFHYVHHDISGQPYADRTELSRQISQAAARSGIG 151
                                        **************************************************************************** PP

                          TIGR02022 153 ltlLpvlYahagFGgaaanegqrrfiddveaflrlvealrkelaaqeearlGlaiHslRAvtaeelaavlqaserq 228
                                        ltl+pvlY+h+gFGg+a+negqrrfi+++e++l+l+++l++ laaq++++lGl++HslRAvt+e+++avl+as+++
  lcl|FitnessBrowser__WCS417:GFF335 152 LTLVPVLYTHSGFGGQAPNEGQRRFINSTEHYLDLQAQLKPILAAQPAQQLGLCFHSLRAVTPEQINAVLAASDKA 227
                                        **************************************************************************** PP

                          TIGR02022 229 lPvHiHvaEqqkEvddClaasgrrPvewLldhaevdarwclvHatHltdeevkllaksgavaglCpttEanLgDGi 304
                                        +PvHiH+aEqqkEvddCla+sg+rP++wL+d++evd+rwclvHatH +++ev+++aks+a+aglC+ttEanLgDGi
  lcl|FitnessBrowser__WCS417:GFF335 228 CPVHIHIAEQQKEVDDCLAWSGKRPLQWLYDNVEVDERWCLVHATHADADEVARMAKSRAIAGLCLTTEANLGDGI 303
                                        **************************************************************************** PP

                          TIGR02022 305 fpaadfvaaggrlgiGsDshvvvdvleElRllEygqRLrdraRnvlaageeasvaralydaAlaggaqalGlaege 380
                                        fpa+df+a+ggr+giGsDshv+++v+eElR+lEygqRLrd++Rn+l++g++++v+r+l+daAl ggaqalG+  g+
  lcl|FitnessBrowser__WCS417:GFF335 304 FPAVDFLAQGGRMGIGSDSHVSLSVVEELRWLEYGQRLRDQRRNRLYRGDQPMVGRTLFDAALDGGAQALGQPIGR 379
                                        **************************************************************************** PP

                          TIGR02022 381 leaGarADlltldledpslagakgdalldsllfaaekaavrdvvvaGrkvvrdgrHaleeeierafakvlrall 454
                                        le+G+rAD+++ld++dp+la+a++d +l+++lfa+++++vrdv+v+G++vvrdg+Ha ee+++raf++vl++ll
  lcl|FitnessBrowser__WCS417:GFF335 380 LEVGKRADWIVLDGNDPYLATATEDGILNRWLFAGGDRQVRDVLVNGKWVVRDGHHAGEEDSNRAFTQVLKDLL 453
                                        ***********************************************************************986 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 8.49
//
[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