Alignments for a candidate for hutF in Phaeobacter inhibens BS107

GapMind for catabolism of small carbon sources

Alignments for a candidate for hutF in Phaeobacter inhibens BS107

Align Formiminoglutamic iminohydrolase (EC 3.5.3.13) (characterized)
to candidate GFF3581 PGA1_c36360 putative formiminoglutamate deiminase

Query= reanno::Phaeo:GFF3581
         (455 letters)



>FitnessBrowser__Phaeo:GFF3581
          Length = 455

 Score =  919 bits (2376), Expect = 0.0
 Identities = 455/455 (100%), Positives = 455/455 (100%)

Query: 1   MQTIFAQHARMPQGWVTDLRLTIEAGKIATLEPGAAVQPQDHRVGALVPALANLHSHSFQ 60
           MQTIFAQHARMPQGWVTDLRLTIEAGKIATLEPGAAVQPQDHRVGALVPALANLHSHSFQ
Sbjct: 1   MQTIFAQHARMPQGWVTDLRLTIEAGKIATLEPGAAVQPQDHRVGALVPALANLHSHSFQ 60

Query: 61  RAMAGMTETRVSGRDSFWSWRKLMYQFVDHLTPEQYEAIAALVFMEMLEAGYASVGEFHY 120
           RAMAGMTETRVSGRDSFWSWRKLMYQFVDHLTPEQYEAIAALVFMEMLEAGYASVGEFHY
Sbjct: 61  RAMAGMTETRVSGRDSFWSWRKLMYQFVDHLTPEQYEAIAALVFMEMLEAGYASVGEFHY 120

Query: 121 VHHQPGGQPYEVLGELSHRVFAAADLTGIGLTHLPVLYTYGGAGQAPLGGGQQRFGNDVT 180
           VHHQPGGQPYEVLGELSHRVFAAADLTGIGLTHLPVLYTYGGAGQAPLGGGQQRFGNDVT
Sbjct: 121 VHHQPGGQPYEVLGELSHRVFAAADLTGIGLTHLPVLYTYGGAGQAPLGGGQQRFGNDVT 180

Query: 181 RYANLLSDCRTTARELLPMDARVGIAPHSLRATAPDELAEVLTLRAESPVHIHIAEQPQE 240
           RYANLLSDCRTTARELLPMDARVGIAPHSLRATAPDELAEVLTLRAESPVHIHIAEQPQE
Sbjct: 181 RYANLLSDCRTTARELLPMDARVGIAPHSLRATAPDELAEVLTLRAESPVHIHIAEQPQE 240

Query: 241 VADIGGWLGERPVQWLLNNCAVDKDWCLIHATHMTEQETHDLARSGAVAGLCPITEANLG 300
           VADIGGWLGERPVQWLLNNCAVDKDWCLIHATHMTEQETHDLARSGAVAGLCPITEANLG
Sbjct: 241 VADIGGWLGERPVQWLLNNCAVDKDWCLIHATHMTEQETHDLARSGAVAGLCPITEANLG 300

Query: 301 DGPFNGVLFQNNGGRFGVGSDSNIRISLSEELRLLEYSQRLRDLARNVMVPEEGSVGAAL 360
           DGPFNGVLFQNNGGRFGVGSDSNIRISLSEELRLLEYSQRLRDLARNVMVPEEGSVGAAL
Sbjct: 301 DGPFNGVLFQNNGGRFGVGSDSNIRISLSEELRLLEYSQRLRDLARNVMVPEEGSVGAAL 360

Query: 361 YLGAACGGAQALGRDAGRLEVGALADLMAFDTTDVTLCALRPDQFLDGLCFAADDSVVRD 420
           YLGAACGGAQALGRDAGRLEVGALADLMAFDTTDVTLCALRPDQFLDGLCFAADDSVVRD
Sbjct: 361 YLGAACGGAQALGRDAGRLEVGALADLMAFDTTDVTLCALRPDQFLDGLCFAADDSVVRD 420

Query: 421 VWSAGRHVVSGGRHANREQIIARYNSAVAALLSAL 455
           VWSAGRHVVSGGRHANREQIIARYNSAVAALLSAL
Sbjct: 421 VWSAGRHVVSGGRHANREQIIARYNSAVAALLSAL 455


Lambda     K      H
   0.321    0.136    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: 846
Number of extensions: 27
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: 455
Length of database: 455
Length adjustment: 33
Effective length of query: 422
Effective length of database: 422
Effective search space:   178084
Effective search space used:   178084
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 GFF3581 PGA1_c36360 (putative 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.16650.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
   1.1e-175  570.7   1.6   1.2e-175  570.5   1.6    1.0  1  lcl|FitnessBrowser__Phaeo:GFF3581  PGA1_c36360 putative formiminogl


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Phaeo:GFF3581  PGA1_c36360 putative formiminoglutamate deiminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  570.5   1.6  1.2e-175  1.2e-175       1     454 [.       1     452 [.       1     453 [. 0.98

  Alignments for each domain:
  == domain 1  score: 570.5 bits;  conditional E-value: 1.2e-175
                          TIGR02022   1 akvyfaerallpdgwaegvrlavaedGrilavetgvsaaedaerlsgvvlpglanlHsHAFqralaGlaevagsga 76 
                                        ++++fa++a +p+gw ++ rl+++ +G+i+++e g++  ++++r++ +++p+lanlHsH Fqra+aG++e++ sg 
  lcl|FitnessBrowser__Phaeo:GFF3581   1 MQTIFAQHARMPQGWVTDLRLTIE-AGKIATLEPGAAVQPQDHRVG-ALVPALANLHSHSFQRAMAGMTETRVSGR 74 
                                        6899*******************9.67**********999998887.9**************************** PP

                          TIGR02022  77 DsFWtWRevmYrlverldPeqleaiarqlyvemlkaGftrvgEFHYlHHaadGtpYadpaelaeriaaAAadaGig 152
                                        DsFW+WR +mY++v++l+Peq+eaia+ +++eml+aG+++vgEFHY+HH+++G+pY+  +el++r+ aAA+ +Gig
  lcl|FitnessBrowser__Phaeo:GFF3581  75 DSFWSWRKLMYQFVDHLTPEQYEAIAALVFMEMLEAGYASVGEFHYVHHQPGGQPYEVLGELSHRVFAAADLTGIG 150
                                        **************************************************************************** PP

                          TIGR02022 153 ltlLpvlYahagFGgaaanegqrrfiddveaflrlvealrkelaaq..eearlGlaiHslRAvtaeelaavlqase 226
                                        lt+LpvlY++ g G a+   gq+rf +dv ++++l++++r++ ++    +ar+G+a+HslRA  ++ela+vl++ +
  lcl|FitnessBrowser__Phaeo:GFF3581 151 LTHLPVLYTYGGAGQAPLGGGQQRFGNDVTRYANLLSDCRTTARELlpMDARVGIAPHSLRATAPDELAEVLTLRA 226
                                        **************999999********************99998643689************************9 PP

                          TIGR02022 227 rqlPvHiHvaEqqkEvddClaasgrrPvewLldhaevdarwclvHatHltdeevkllaksgavaglCpttEanLgD 302
                                        ++ PvHiH+aEq++Ev d   + g+rPv+wLl++  vd+ wcl+HatH+t++e++ la+sgavaglCp+tEanLgD
  lcl|FitnessBrowser__Phaeo:GFF3581 227 ES-PVHIHIAEQPQEVADIGGWLGERPVQWLLNNCAVDKDWCLIHATHMTEQETHDLARSGAVAGLCPITEANLGD 301
                                        97.************************************************************************* PP

                          TIGR02022 303 GifpaadfvaaggrlgiGsDshvvvdvleElRllEygqRLrdraRnvlaageeasvaralydaAlaggaqalGlae 378
                                        G f+ + f+++ggr+g+GsDs++ +++ eElRllEy+qRLrd aRnv+   ee sv++aly  A+ ggaqalG+++
  lcl|FitnessBrowser__Phaeo:GFF3581 302 GPFNGVLFQNNGGRFGVGSDSNIRISLSEELRLLEYSQRLRDLARNVMVP-EEGSVGAALYLGAACGGAQALGRDA 376
                                        *************************************************8.669********************** PP

                          TIGR02022 379 geleaGarADlltldledpslagakgdalldsllfaaekaavrdvvvaGrkvvrdgrHaleeeierafakvlrall 454
                                        g+le+Ga ADl+  d+ d++l + ++d+ ld l faa+++ vrdv+ aGr+vv++grHa++e+i  ++  ++ all
  lcl|FitnessBrowser__Phaeo:GFF3581 377 GRLEVGALADLMAFDTTDVTLCALRPDQFLDGLCFAADDSVVRDVWSAGRHVVSGGRHANREQIIARYNSAVAALL 452
                                        *********************************************************************9999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (455 nodes)
Target sequences:                          1  (455 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: 8.06
//
[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