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.4349.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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 12.74
//
[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:

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:

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:

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:

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