Alignments for a candidate for hutF in Sinorhizobium meliloti 1021

GapMind for catabolism of small carbon sources

Alignments for a candidate for hutF in Sinorhizobium meliloti 1021

Align Formiminoglutamic iminohydrolase (EC 3.5.3.13) (characterized)
to candidate SMc00673 SMc00673 N-formimino-L-glutamate deiminase

Query= reanno::Smeli:SMc00673
         (461 letters)



>FitnessBrowser__Smeli:SMc00673
          Length = 461

 Score =  929 bits (2402), Expect = 0.0
 Identities = 461/461 (100%), Positives = 461/461 (100%)

Query: 1   MTASSAHRLFAEQALLPTGWSENVAISVDAAGRILAVEAGQSKAPGDEHLSGPIVPAMAN 60
           MTASSAHRLFAEQALLPTGWSENVAISVDAAGRILAVEAGQSKAPGDEHLSGPIVPAMAN
Sbjct: 1   MTASSAHRLFAEQALLPTGWSENVAISVDAAGRILAVEAGQSKAPGDEHLSGPIVPAMAN 60

Query: 61  LHSHAFQRAMAGLAEVAGTGDDSFWTWREEMYRTVGLVDPDDLEAIAAKLYVEMLKGGFG 120
           LHSHAFQRAMAGLAEVAGTGDDSFWTWREEMYRTVGLVDPDDLEAIAAKLYVEMLKGGFG
Sbjct: 61  LHSHAFQRAMAGLAEVAGTGDDSFWTWREEMYRTVGLVDPDDLEAIAAKLYVEMLKGGFG 120

Query: 121 RVVEFHYLHHQLDGTPYADPAEMSLRILRAAQTTGIGLTHLPVFYAHANFGGAAPSAGQR 180
           RVVEFHYLHHQLDGTPYADPAEMSLRILRAAQTTGIGLTHLPVFYAHANFGGAAPSAGQR
Sbjct: 121 RVVEFHYLHHQLDGTPYADPAEMSLRILRAAQTTGIGLTHLPVFYAHANFGGAAPSAGQR 180

Query: 181 PFLHDPDRFLALLERLSPACNATGARLGYAIHSLRAATPEEMREILQSSPLTGPIHIHVA 240
           PFLHDPDRFLALLERLSPACNATGARLGYAIHSLRAATPEEMREILQSSPLTGPIHIHVA
Sbjct: 181 PFLHDPDRFLALLERLSPACNATGARLGYAIHSLRAATPEEMREILQSSPLTGPIHIHVA 240

Query: 241 EQPREVEDCLAWSGRRPVEWLLDNMPVDERWCAIHATHMTPDETRRLAHSGAVAGLCPAT 300
           EQPREVEDCLAWSGRRPVEWLLDNMPVDERWCAIHATHMTPDETRRLAHSGAVAGLCPAT
Sbjct: 241 EQPREVEDCLAWSGRRPVEWLLDNMPVDERWCAIHATHMTPDETRRLAHSGAVAGLCPAT 300

Query: 301 EANLGDGIFPAVDFVAAGGRFGVGTDSHVATSVAEELRLLEYGQRLRDRRRNRLAAPGAS 360
           EANLGDGIFPAVDFVAAGGRFGVGTDSHVATSVAEELRLLEYGQRLRDRRRNRLAAPGAS
Sbjct: 301 EANLGDGIFPAVDFVAAGGRFGVGTDSHVATSVAEELRLLEYGQRLRDRRRNRLAAPGAS 360

Query: 361 VGRSIFDAALAGGAQAAGQAAGMEEPGIRVGAMADLVVLDGSNPYIAAASGNQILDRWLF 420
           VGRSIFDAALAGGAQAAGQAAGMEEPGIRVGAMADLVVLDGSNPYIAAASGNQILDRWLF
Sbjct: 361 VGRSIFDAALAGGAQAAGQAAGMEEPGIRVGAMADLVVLDGSNPYIAAASGNQILDRWLF 420

Query: 421 ALGGDTVRDVMIAGEWKIRNGRHDREEDIDRAFARVLNKLK 461
           ALGGDTVRDVMIAGEWKIRNGRHDREEDIDRAFARVLNKLK
Sbjct: 421 ALGGDTVRDVMIAGEWKIRNGRHDREEDIDRAFARVLNKLK 461


Lambda     K      H
   0.320    0.135    0.412 

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: 906
Number of extensions: 16
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: 461
Length of database: 461
Length adjustment: 33
Effective length of query: 428
Effective length of database: 428
Effective search space:   183184
Effective search space used:   183184
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 SMc00673 SMc00673 (N-formimino-L-glutamate 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.11674.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   3.3e-227  740.5   0.9   3.7e-227  740.3   0.9    1.0  1  lcl|FitnessBrowser__Smeli:SMc00673  SMc00673 N-formimino-L-glutamate


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Smeli:SMc00673  SMc00673 N-formimino-L-glutamate deiminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  740.3   0.9  3.7e-227  3.7e-227       2     454 ..       7     461 .]       6     461 .] 0.99

  Alignments for each domain:
  == domain 1  score: 740.3 bits;  conditional E-value: 3.7e-227
                           TIGR02022   2 kvyfaerallpdgwaegvrlavaedGrilavetgvsaaedaerlsgvvlpglanlHsHAFqralaGlaevagsga 76 
                                         + +fae+allp+gw+e+v+++v+++Grilave+g+s+a+++e+lsg+++p++anlHsHAFqra+aGlaevag+g+
  lcl|FitnessBrowser__Smeli:SMc00673   7 HRLFAEQALLPTGWSENVAISVDAAGRILAVEAGQSKAPGDEHLSGPIVPAMANLHSHAFQRAMAGLAEVAGTGD 81 
                                         689************************************************************************ PP

                           TIGR02022  77 DsFWtWRevmYrlverldPeqleaiarqlyvemlkaGftrvgEFHYlHHaadGtpYadpaelaeriaaAAadaGi 151
                                         DsFWtWRe mYr+v  +dP++leaia++lyvemlk+Gf+rv+EFHYlHH+ dGtpYadpae++ ri++AA+++Gi
  lcl|FitnessBrowser__Smeli:SMc00673  82 DSFWTWREEMYRTVGLVDPDDLEAIAAKLYVEMLKGGFGRVVEFHYLHHQLDGTPYADPAEMSLRILRAAQTTGI 156
                                         *************************************************************************** PP

                           TIGR02022 152 gltlLpvlYahagFGgaaanegqrrfiddveaflrlvealrkelaaqeearlGlaiHslRAvtaeelaavlqase 226
                                         glt+Lpv+Yaha+FGgaa+++gqr+f++d+++fl+l+e+l+++++ ++ arlG+aiHslRA+t+ee++++lq+s+
  lcl|FitnessBrowser__Smeli:SMc00673 157 GLTHLPVFYAHANFGGAAPSAGQRPFLHDPDRFLALLERLSPACN-ATGARLGYAIHSLRAATPEEMREILQSSP 230
                                         *******************************************99.789************************** PP

                           TIGR02022 227 rqlPvHiHvaEqqkEvddClaasgrrPvewLldhaevdarwclvHatHltdeevkllaksgavaglCpttEanLg 301
                                          + P+HiHvaEq++Ev+dCla+sgrrPvewLld+++vd+rwc++HatH+t++e+++la+sgavaglCp+tEanLg
  lcl|FitnessBrowser__Smeli:SMc00673 231 LTGPIHIHVAEQPREVEDCLAWSGRRPVEWLLDNMPVDERWCAIHATHMTPDETRRLAHSGAVAGLCPATEANLG 305
                                         *************************************************************************** PP

                           TIGR02022 302 DGifpaadfvaaggrlgiGsDshvvvdvleElRllEygqRLrdraRnvlaageeasvaralydaAlaggaqalGl 376
                                         DGifpa+dfvaaggr+g+G+Dshv+++v+eElRllEygqRLrdr+Rn+laa ++asv+r+++daAlaggaqa+G+
  lcl|FitnessBrowser__Smeli:SMc00673 306 DGIFPAVDFVAAGGRFGVGTDSHVATSVAEELRLLEYGQRLRDRRRNRLAA-PGASVGRSIFDAALAGGAQAAGQ 379
                                         **************************************************7.99*****************9999 PP

                           TIGR02022 377 ae....geleaGarADlltldledpslagakgdalldsllfaaekaavrdvvvaGrkvvrdgrHaleeeierafa 447
                                         a+     ++++Ga+ADl++ld+++p++a+a+g+++ld++lfa ++++vrdv++aG++++r+grH++ee+i+rafa
  lcl|FitnessBrowser__Smeli:SMc00673 380 AAgmeePGIRVGAMADLVVLDGSNPYIAAASGNQILDRWLFALGGDTVRDVMIAGEWKIRNGRHDREEDIDRAFA 454
                                         88666689******************************************************************* PP

                           TIGR02022 448 kvlrall 454
                                         +vl++l+
  lcl|FitnessBrowser__Smeli:SMc00673 455 RVLNKLK 461
                                         ****985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (455 nodes)
Target sequences:                          1  (461 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 11.49
//
[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