Alignments for a candidate for hutF in Pseudomonas fluorescens FW300-N1B4

GapMind for catabolism of small carbon sources

Alignments for a candidate for hutF in Pseudomonas fluorescens FW300-N1B4

Align Formiminoglutamic iminohydrolase (EC 3.5.3.13) (characterized)
to candidate Pf1N1B4_1591 Formiminoglutamic iminohydrolase (EC 3.5.3.13)

Query= reanno::pseudo1_N1B4:Pf1N1B4_1591
         (454 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1591
          Length = 454

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

Query: 1   MSAFFAERALLPSGWANNVRLEVSADGVLTHIQADSHADDAERLSGPLLPGMPNLHSHAF 60
           MSAFFAERALLPSGWANNVRLEVSADGVLTHIQADSHADDAERLSGPLLPGMPNLHSHAF
Sbjct: 1   MSAFFAERALLPSGWANNVRLEVSADGVLTHIQADSHADDAERLSGPLLPGMPNLHSHAF 60

Query: 61  QRAMAGLAEVAGNPNDSFWTWRDLMYRLVGKISPDQLGVIARQLYIEMLKAGYTSVAEFH 120
           QRAMAGLAEVAGNPNDSFWTWRDLMYRLVGKISPDQLGVIARQLYIEMLKAGYTSVAEFH
Sbjct: 61  QRAMAGLAEVAGNPNDSFWTWRDLMYRLVGKISPDQLGVIARQLYIEMLKAGYTSVAEFH 120

Query: 121 YVHHDTSGQPYADPAELALRISQAASSAGIGLTLLPVLYSHSGFGGQAPNEGQRRFINST 180
           YVHHDTSGQPYADPAELALRISQAASSAGIGLTLLPVLYSHSGFGGQAPNEGQRRFINST
Sbjct: 121 YVHHDTSGQPYADPAELALRISQAASSAGIGLTLLPVLYSHSGFGGQAPNEGQRRFINST 180

Query: 181 ENYLKLQSRLQPILAQQPAQALGLCFHSLRAVTPQQISEVLAASDKQCPVHIHIAEQQKE 240
           ENYLKLQSRLQPILAQQPAQALGLCFHSLRAVTPQQISEVLAASDKQCPVHIHIAEQQKE
Sbjct: 181 ENYLKLQSRLQPILAQQPAQALGLCFHSLRAVTPQQISEVLAASDKQCPVHIHIAEQQKE 240

Query: 241 VDDCLSWSGRRPLQWLYENTDVDQRWCLVHATHANPEEVTLMAKSRAIAGLCLTTEANLG 300
           VDDCLSWSGRRPLQWLYENTDVDQRWCLVHATHANPEEVTLMAKSRAIAGLCLTTEANLG
Sbjct: 241 VDDCLSWSGRRPLQWLYENTDVDQRWCLVHATHANPEEVTLMAKSRAIAGLCLTTEANLG 300

Query: 301 DGIFPAVDFLAQGGRMGIGSDSHVSLSVVEELRWLEYGQRLRDQRRNRLYGADQPMVGRT 360
           DGIFPAVDFLAQGGRMGIGSDSHVSLSVVEELRWLEYGQRLRDQRRNRLYGADQPMVGRT
Sbjct: 301 DGIFPAVDFLAQGGRMGIGSDSHVSLSVVEELRWLEYGQRLRDQRRNRLYGADQPMVGRT 360

Query: 361 LYDAALDGGAQALGQPIGALEVGKRADWLVLDGNDPYLATASGDGILNRWLFAGGDRQVR 420
           LYDAALDGGAQALGQPIGALEVGKRADWLVLDGNDPYLATASGDGILNRWLFAGGDRQVR
Sbjct: 361 LYDAALDGGAQALGQPIGALEVGKRADWLVLDGNDPYLATASGDGILNRWLFAGGDRQVR 420

Query: 421 DVLVNGQWVVRDGRHAGEEESNRAFTQVLRDLLG 454
           DVLVNGQWVVRDGRHAGEEESNRAFTQVLRDLLG
Sbjct: 421 DVLVNGQWVVRDGRHAGEEESNRAFTQVLRDLLG 454


Lambda     K      H
   0.319    0.135    0.413 

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: 902
Number of extensions: 20
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 Pf1N1B4_1591 (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.8868.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                      -----------
   1.4e-229  748.4   0.1   1.5e-229  748.2   0.1    1.0  1  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1591  Formiminoglutamic iminohydrolase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1591  Formiminoglutamic iminohydrolase (EC 3.5.3.13)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  748.2   0.1  1.5e-229  1.5e-229       1     454 [.       1     453 [.       1     454 [] 0.99

  Alignments for each domain:
  == domain 1  score: 748.2 bits;  conditional E-value: 1.5e-229
                                      TIGR02022   1 akvyfaerallpdgwaegvrlavaedGrilavetgvsaaedaerlsgvvlpglanlHsHAFqra 64 
                                                    ++++faerallp gwa++vrl+v++dG ++ +++++  a+daerlsg++lpg++nlHsHAFqra
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1591   1 MSAFFAERALLPSGWANNVRLEVSADGVLTHIQADSH-ADDAERLSGPLLPGMPNLHSHAFQRA 63 
                                                    5789****************************98888.************************** PP

                                      TIGR02022  65 laGlaevagsgaDsFWtWRevmYrlverldPeqleaiarqlyvemlkaGftrvgEFHYlHHaad 128
                                                    +aGlaevag+++DsFWtWR++mYrlv +++P+ql +iarqly+emlkaG+t+v+EFHY+HH+++
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1591  64 MAGLAEVAGNPNDSFWTWRDLMYRLVGKISPDQLGVIARQLYIEMLKAGYTSVAEFHYVHHDTS 127
                                                    **************************************************************** PP

                                      TIGR02022 129 GtpYadpaelaeriaaAAadaGigltlLpvlYahagFGgaaanegqrrfiddveaflrlvealr 192
                                                    G+pYadpaela ri++AA+ aGigltlLpvlY+h+gFGg+a+negqrrfi+++e++l+l+++l+
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1591 128 GQPYADPAELALRISQAASSAGIGLTLLPVLYSHSGFGGQAPNEGQRRFINSTENYLKLQSRLQ 191
                                                    **************************************************************** PP

                                      TIGR02022 193 kelaaqeearlGlaiHslRAvtaeelaavlqaserqlPvHiHvaEqqkEvddClaasgrrPvew 256
                                                    + la+q+++ lGl++HslRAvt++++++vl+as++q+PvHiH+aEqqkEvddCl +sgrrP++w
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1591 192 PILAQQPAQALGLCFHSLRAVTPQQISEVLAASDKQCPVHIHIAEQQKEVDDCLSWSGRRPLQW 255
                                                    **************************************************************** PP

                                      TIGR02022 257 LldhaevdarwclvHatHltdeevkllaksgavaglCpttEanLgDGifpaadfvaaggrlgiG 320
                                                    L+++++vd+rwclvHatH ++eev+l+aks+a+aglC+ttEanLgDGifpa+df+a+ggr+giG
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1591 256 LYENTDVDQRWCLVHATHANPEEVTLMAKSRAIAGLCLTTEANLGDGIFPAVDFLAQGGRMGIG 319
                                                    **************************************************************** PP

                                      TIGR02022 321 sDshvvvdvleElRllEygqRLrdraRnvlaageeasvaralydaAlaggaqalGlaegeleaG 384
                                                    sDshv+++v+eElR+lEygqRLrd++Rn+l+  ++++v+r+lydaAl ggaqalG+  g+le+G
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1591 320 SDSHVSLSVVEELRWLEYGQRLRDQRRNRLYGADQPMVGRTLYDAALDGGAQALGQPIGALEVG 383
                                                    **************************************************************** PP

                                      TIGR02022 385 arADlltldledpslagakgdalldsllfaaekaavrdvvvaGrkvvrdgrHaleeeierafak 448
                                                    +rAD+l+ld++dp+la+a+gd +l+++lfa+++++vrdv+v+G++vvrdgrHa eee++raf++
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1591 384 KRADWLVLDGNDPYLATASGDGILNRWLFAGGDRQVRDVLVNGQWVVRDGRHAGEEESNRAFTQ 447
                                                    **************************************************************** PP

                                      TIGR02022 449 vlrall 454
                                                    vlr+ll
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1591 448 VLRDLL 453
                                                    ***996 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 10.38
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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