Alignments for a candidate for hutF in Pseudomonas fluorescens GW456-L13

GapMind for catabolism of small carbon sources

Alignments for a candidate for hutF in Pseudomonas fluorescens GW456-L13

Align Formiminoglutamic iminohydrolase (EC 3.5.3.13) (characterized)
to candidate PfGW456L13_330 Formiminoglutamic iminohydrolase (EC 3.5.3.13)

Query= reanno::pseudo13_GW456_L13:PfGW456L13_330
         (454 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_330
          Length = 454

 Score =  920 bits (2377), Expect = 0.0
 Identities = 454/454 (100%), Positives = 454/454 (100%)

Query: 1   MSAFFAERALLPSGWANNVRLEVSADGVLTHIQADSNADGAERLSGPLLPGMPNLHSHAF 60
           MSAFFAERALLPSGWANNVRLEVSADGVLTHIQADSNADGAERLSGPLLPGMPNLHSHAF
Sbjct: 1   MSAFFAERALLPSGWANNVRLEVSADGVLTHIQADSNADGAERLSGPLLPGMPNLHSHAF 60

Query: 61  QRAMAGLAEVAGNPNDSFWTWRDLMYRLVGKISPEQLGVIARQLYIEMLKAGYTSVAEFH 120
           QRAMAGLAEVAGNPNDSFWTWRDLMYRLVGKISPEQLGVIARQLYIEMLKAGYTSVAEFH
Sbjct: 61  QRAMAGLAEVAGNPNDSFWTWRDLMYRLVGKISPEQLGVIARQLYIEMLKAGYTSVAEFH 120

Query: 121 YVHHDISGQPYADPAELALRISQAAGSAGIGLTLLPVLYSHSGFGGQTPNEGQRRFINST 180
           YVHHDISGQPYADPAELALRISQAAGSAGIGLTLLPVLYSHSGFGGQTPNEGQRRFINST
Sbjct: 121 YVHHDISGQPYADPAELALRISQAAGSAGIGLTLLPVLYSHSGFGGQTPNEGQRRFINST 180

Query: 181 ENYLKLQSRLQPLLAQQPAQALGLCFHSLRAVTPQQISEVLAASDKQCPVHIHIAEQQKE 240
           ENYLKLQSRLQPLLAQQPAQALGLCFHSLRAVTPQQISEVLAASDKQCPVHIHIAEQQKE
Sbjct: 181 ENYLKLQSRLQPLLAQQPAQALGLCFHSLRAVTPQQISEVLAASDKQCPVHIHIAEQQKE 240

Query: 241 VDDCLTWSGRRPLQWLYENVEVDQRWCLVHATHANPEEVTSMARSRAIAGLCLTTEANLG 300
           VDDCLTWSGRRPLQWLYENVEVDQRWCLVHATHANPEEVTSMARSRAIAGLCLTTEANLG
Sbjct: 241 VDDCLTWSGRRPLQWLYENVEVDQRWCLVHATHANPEEVTSMARSRAIAGLCLTTEANLG 300

Query: 301 DGIFPAVDFLAQGGRMGIGSDSHVSLSVVEELRWLEYGQRLRDQRRNRLYGADQPMVGRT 360
           DGIFPAVDFLAQGGRMGIGSDSHVSLSVVEELRWLEYGQRLRDQRRNRLYGADQPMVGRT
Sbjct: 301 DGIFPAVDFLAQGGRMGIGSDSHVSLSVVEELRWLEYGQRLRDQRRNRLYGADQPMVGRT 360

Query: 361 LFDAALDGGAQALGQPIGALEVGKRADWLVLDGNDPYLATANGDGILNRWLFAGGDRQVR 420
           LFDAALDGGAQALGQPIGALEVGKRADWLVLDGNDPYLATANGDGILNRWLFAGGDRQVR
Sbjct: 361 LFDAALDGGAQALGQPIGALEVGKRADWLVLDGNDPYLATANGDGILNRWLFAGGDRQVR 420

Query: 421 DVLVNGQWVVRDGRHADEEESNRAFTQVLRELLG 454
           DVLVNGQWVVRDGRHADEEESNRAFTQVLRELLG
Sbjct: 421 DVLVNGQWVVRDGRHADEEESNRAFTQVLRELLG 454


Lambda     K      H
   0.319    0.135    0.414 

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: 932
Number of extensions: 18
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 PfGW456L13_330 (Formiminoglutamic iminohydrolase (EC 3.5.3.13))
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.11845.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                              -----------
   2.9e-228  744.0   0.1   3.3e-228  743.8   0.1    1.0  1  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_330  Formiminoglutamic iminohydrolase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_330  Formiminoglutamic iminohydrolase (EC 3.5.3.13)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  743.8   0.1  3.3e-228  3.3e-228       1     454 [.       1     453 [.       1     454 [] 0.99

  Alignments for each domain:
  == domain 1  score: 743.8 bits;  conditional E-value: 3.3e-228
                                              TIGR02022   1 akvyfaerallpdgwaegvrlavaedGrilavetgvsaaedaerlsgvvlpglanl 56 
                                                            ++++faerallp gwa++vrl+v++dG ++ +++++  a++aerlsg++lpg++nl
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_330   1 MSAFFAERALLPSGWANNVRLEVSADGVLTHIQADSN-ADGAERLSGPLLPGMPNL 55 
                                                            5789****************************98888.****************** PP

                                              TIGR02022  57 HsHAFqralaGlaevagsgaDsFWtWRevmYrlverldPeqleaiarqlyvemlka 112
                                                            HsHAFqra+aGlaevag+++DsFWtWR++mYrlv +++Peql +iarqly+emlka
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_330  56 HSHAFQRAMAGLAEVAGNPNDSFWTWRDLMYRLVGKISPEQLGVIARQLYIEMLKA 111
                                                            ******************************************************** PP

                                              TIGR02022 113 GftrvgEFHYlHHaadGtpYadpaelaeriaaAAadaGigltlLpvlYahagFGga 168
                                                            G+t+v+EFHY+HH+ +G+pYadpaela ri++AA  aGigltlLpvlY+h+gFGg+
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_330 112 GYTSVAEFHYVHHDISGQPYADPAELALRISQAAGSAGIGLTLLPVLYSHSGFGGQ 167
                                                            ******************************************************** PP

                                              TIGR02022 169 aanegqrrfiddveaflrlvealrkelaaqeearlGlaiHslRAvtaeelaavlqa 224
                                                            ++negqrrfi+++e++l+l+++l++ la+q+++ lGl++HslRAvt++++++vl+a
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_330 168 TPNEGQRRFINSTENYLKLQSRLQPLLAQQPAQALGLCFHSLRAVTPQQISEVLAA 223
                                                            ******************************************************** PP

                                              TIGR02022 225 serqlPvHiHvaEqqkEvddClaasgrrPvewLldhaevdarwclvHatHltdeev 280
                                                            s++q+PvHiH+aEqqkEvddCl +sgrrP++wL++++evd+rwclvHatH ++eev
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_330 224 SDKQCPVHIHIAEQQKEVDDCLTWSGRRPLQWLYENVEVDQRWCLVHATHANPEEV 279
                                                            ******************************************************** PP

                                              TIGR02022 281 kllaksgavaglCpttEanLgDGifpaadfvaaggrlgiGsDshvvvdvleElRll 336
                                                            + +a+s+a+aglC+ttEanLgDGifpa+df+a+ggr+giGsDshv+++v+eElR+l
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_330 280 TSMARSRAIAGLCLTTEANLGDGIFPAVDFLAQGGRMGIGSDSHVSLSVVEELRWL 335
                                                            ******************************************************** PP

                                              TIGR02022 337 EygqRLrdraRnvlaageeasvaralydaAlaggaqalGlaegeleaGarADlltl 392
                                                            EygqRLrd++Rn+l+  ++++v+r+l+daAl ggaqalG+  g+le+G+rAD+l+l
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_330 336 EYGQRLRDQRRNRLYGADQPMVGRTLFDAALDGGAQALGQPIGALEVGKRADWLVL 391
                                                            ******************************************************** PP

                                              TIGR02022 393 dledpslagakgdalldsllfaaekaavrdvvvaGrkvvrdgrHaleeeierafak 448
                                                            d++dp+la+a+gd +l+++lfa+++++vrdv+v+G++vvrdgrHa+eee++raf++
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_330 392 DGNDPYLATANGDGILNRWLFAGGDRQVRDVLVNGQWVVRDGRHADEEESNRAFTQ 447
                                                            ******************************************************** PP

                                              TIGR02022 449 vlrall 454
                                                            vlr+ll
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_330 448 VLRELL 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: 9.04
//
[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