Alignments for a candidate for hutF in Acidovorax sp. GW101-3H11

GapMind for catabolism of small carbon sources

Alignments for a candidate for hutF in Acidovorax sp. GW101-3H11

Align Formiminoglutamic iminohydrolase (EC 3.5.3.13) (characterized)
to candidate Ac3H11_2549 Formiminoglutamic iminohydrolase (EC 3.5.3.13)

Query= reanno::acidovorax_3H11:Ac3H11_2549
         (464 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_2549
          Length = 464

 Score =  931 bits (2405), Expect = 0.0
 Identities = 464/464 (100%), Positives = 464/464 (100%)

Query: 1   MSEPLQRQLFAADALLPTGWARDVLVAWDGAGRITAVTPNAQPNGAAVAPGPLLPGMPNL 60
           MSEPLQRQLFAADALLPTGWARDVLVAWDGAGRITAVTPNAQPNGAAVAPGPLLPGMPNL
Sbjct: 1   MSEPLQRQLFAADALLPTGWARDVLVAWDGAGRITAVTPNAQPNGAAVAPGPLLPGMPNL 60

Query: 61  HSHAFQRAFAGLTEYRGESQDSFWSWRNLMYRFAARITPESLEAIATWLYVEMLEAGYTS 120
           HSHAFQRAFAGLTEYRGESQDSFWSWRNLMYRFAARITPESLEAIATWLYVEMLEAGYTS
Sbjct: 61  HSHAFQRAFAGLTEYRGESQDSFWSWRNLMYRFAARITPESLEAIATWLYVEMLEAGYTS 120

Query: 121 VCEFHYVHHDQDGRPYADDATLSLALLRAAKSAGIGITLLPVLYQTSGFGAKPPRADQAR 180
           VCEFHYVHHDQDGRPYADDATLSLALLRAAKSAGIGITLLPVLYQTSGFGAKPPRADQAR
Sbjct: 121 VCEFHYVHHDQDGRPYADDATLSLALLRAAKSAGIGITLLPVLYQTSGFGAKPPRADQAR 180

Query: 181 FIRSTDNMLSLLERLAPATRALGGILGLAPHSLRAVPPDSLAAAVQGLTALNPQAPIHIH 240
           FIRSTDNMLSLLERLAPATRALGGILGLAPHSLRAVPPDSLAAAVQGLTALNPQAPIHIH
Sbjct: 181 FIRSTDNMLSLLERLAPATRALGGILGLAPHSLRAVPPDSLAAAVQGLTALNPQAPIHIH 240

Query: 241 IAEQTQEVEDCIAWSGQRPVQWLLEHAPVDERWCLVHATHMTPQEYADAARTGAVAGICP 300
           IAEQTQEVEDCIAWSGQRPVQWLLEHAPVDERWCLVHATHMTPQEYADAARTGAVAGICP
Sbjct: 241 IAEQTQEVEDCIAWSGQRPVQWLLEHAPVDERWCLVHATHMTPQEYADAARTGAVAGICP 300

Query: 301 TTEANLGDGIFDMPLWLQHGGRWGVGSDSHACVNAAEELLMLEYGQRLSLRQRNVLASRS 360
           TTEANLGDGIFDMPLWLQHGGRWGVGSDSHACVNAAEELLMLEYGQRLSLRQRNVLASRS
Sbjct: 301 TTEANLGDGIFDMPLWLQHGGRWGVGSDSHACVNAAEELLMLEYGQRLSLRQRNVLASRS 360

Query: 361 QAEVATAMTLQAVQGGAQASGRSVSGLAVGQQADLVALDARHVALAGLPAPSMLSSHVFG 420
           QAEVATAMTLQAVQGGAQASGRSVSGLAVGQQADLVALDARHVALAGLPAPSMLSSHVFG
Sbjct: 361 QAEVATAMTLQAVQGGAQASGRSVSGLAVGQQADLVALDARHVALAGLPAPSMLSSHVFG 420

Query: 421 SHRTSAIDSLWVAGVLRVAQGRHALHDAAAQAFVAARSTTIAAD 464
           SHRTSAIDSLWVAGVLRVAQGRHALHDAAAQAFVAARSTTIAAD
Sbjct: 421 SHRTSAIDSLWVAGVLRVAQGRHALHDAAAQAFVAARSTTIAAD 464


Lambda     K      H
   0.320    0.132    0.403 

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: 915
Number of extensions: 36
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: 464
Length of database: 464
Length adjustment: 33
Effective length of query: 431
Effective length of database: 431
Effective search space:   185761
Effective search space used:   185761
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 Ac3H11_2549 (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.8927.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                        -----------
   2.1e-181  589.6   4.7   2.4e-181  589.3   4.7    1.0  1  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2549  Formiminoglutamic iminohydrolase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2549  Formiminoglutamic iminohydrolase (EC 3.5.3.13)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  589.3   4.7  2.4e-181  2.4e-181       2     449 ..       7     456 ..       6     462 .. 0.97

  Alignments for each domain:
  == domain 1  score: 589.3 bits;  conditional E-value: 2.4e-181
                                        TIGR02022   2 kvyfaerallpdgwaegvrlavaedGrilavetgvsaaedaerlsgvvlpglanlHsHAFqr 63 
                                                      + +fa+ allp+gwa++v +a + +Gri+av  +++ +++a++  g++lpg++nlHsHAFqr
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2549   7 RQLFAADALLPTGWARDVLVAWDGAGRITAVTPNAQ-PNGAAVAPGPLLPGMPNLHSHAFQR 67 
                                                      5789***************************77777.9************************ PP

                                        TIGR02022  64 alaGlaevagsgaDsFWtWRevmYrlverldPeqleaiarqlyvemlkaGftrvgEFHYlHH 125
                                                      a+aGl+e++g+++DsFW+WR++mYr+++r++Pe+leaia  lyveml+aG+t+v EFHY+HH
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2549  68 AFAGLTEYRGESQDSFWSWRNLMYRFAARITPESLEAIATWLYVEMLEAGYTSVCEFHYVHH 129
                                                      ************************************************************** PP

                                        TIGR02022 126 aadGtpYadpaelaeriaaAAadaGigltlLpvlYahagFGgaaanegqrrfiddveaflrl 187
                                                      ++dG pYad a+l+ ++++AA+ aGig+tlLpvlY  +gFG++++ + q rfi ++++ l l
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2549 130 DQDGRPYADDATLSLALLRAAKSAGIGITLLPVLYQTSGFGAKPPRADQARFIRSTDNMLSL 191
                                                      ************************************************************** PP

                                        TIGR02022 188 vealrkelaaqeearlGlaiHslRAvtaeelaavlq...aserqlPvHiHvaEqqkEvddCl 246
                                                      +e+l+++ +a     lGla+HslRAv+++ laa +q   a + q+P+HiH+aEq++Ev+dC+
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2549 192 LERLAPATRA-LGGILGLAPHSLRAVPPDSLAAAVQgltALNPQAPIHIHIAEQTQEVEDCI 252
                                                      *****99995.5678*****************9988655667899***************** PP

                                        TIGR02022 247 aasgrrPvewLldhaevdarwclvHatHltdeevkllaksgavaglCpttEanLgDGifpaa 308
                                                      a+sg+rPv+wLl+ha+vd+rwclvHatH+t++e +  a++gavag+CpttEanLgDGif + 
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2549 253 AWSGQRPVQWLLEHAPVDERWCLVHATHMTPQEYADAARTGAVAGICPTTEANLGDGIFDMP 314
                                                      ************************************************************** PP

                                        TIGR02022 309 dfvaaggrlgiGsDshvvvdvleElRllEygqRLrdraRnvlaageeasvaralydaAlagg 370
                                                       ++++ggr+g+GsDsh+ v+++eEl +lEygqRL+ r+Rnvla+ ++a va+a+  +A+ gg
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2549 315 LWLQHGGRWGVGSDSHACVNAAEELLMLEYGQRLSLRQRNVLASRSQAEVATAMTLQAVQGG 376
                                                      ************************************************************** PP

                                        TIGR02022 371 aqalGlaegeleaGarADlltldledpslagakgdalldsllfaae.kaavrdvvvaGrkvv 431
                                                      aqa G++ ++l++G++ADl+ ld+ +++lag    ++l s +f+++ ++a++  +vaG   v
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2549 377 AQASGRSVSGLAVGQQADLVALDARHVALAGLPAPSMLSSHVFGSHrTSAIDSLWVAGVLRV 438
                                                      *******************************************98516789*********** PP

                                        TIGR02022 432 rdgrHaleeeierafakv 449
                                                       +grHal++++++af+++
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2549 439 AQGRHALHDAAAQAFVAA 456
                                                      ***************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (455 nodes)
Target sequences:                          1  (464 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: 00:00:00.01
# Mc/sec: 10.91
//
[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