Alignments for a candidate for hutF in Nocardioides dokdonensis FR1436

GapMind for catabolism of small carbon sources

Alignments for a candidate for hutF in Nocardioides dokdonensis FR1436

Align formimidoylglutamate deiminase (EC 3.5.3.13) (characterized)
to candidate WP_068106976.1 I601_RS04780 formimidoylglutamate deiminase

Query= BRENDA::Q9HU77
         (453 letters)



>NCBI__GCF_001653335.1:WP_068106976.1
          Length = 456

 Score =  231 bits (588), Expect = 5e-65
 Identities = 150/388 (38%), Positives = 202/388 (52%), Gaps = 17/388 (4%)

Query: 43  RLGGAVLPGMPNLHSHAFQRAMAGLAEVAGNPNDSFWTWRELMYRMVARLSPEQIEVIAC 102
           R+ G  LPG+ N HSHAF RA+ G  +  G    +FWTWRE MY +  RL P+    +A 
Sbjct: 60  RVPGLTLPGLANQHSHAFHRALRGRTQRGGG---TFWTWREQMYDLAGRLDPDDHLDLAT 116

Query: 103 QLYIEMLKAGYTAVAEFHYVHHDLDGRSYADPAELSLRISRAASAAGIGLTLLPVLYSHA 162
            LY EM+  G T V EFHY+HH  DGR+YA+P E  L +  AA  AG+ + LL   Y  +
Sbjct: 117 ALYREMVAVGITTVGEFHYLHHAPDGRAYAEPNETGLVLVEAARRAGLRIALLDTCYLSS 176

Query: 163 GFGGQPASEGQRRFING-SEAYLELLQRLRAPLEAAGH-SLGLCFHSLRAVTPQQIATVL 220
           GFG  P    Q R+ +G ++ + + ++ L A   A  H  +G   HS+RAV   Q+ TV+
Sbjct: 177 GFGA-PVEGAQVRYTDGDADRWAQRVEALDAATGADDHVVVGAAVHSVRAVPRDQLPTVV 235

Query: 221 AAGHDDLPVHIHIAEQQKEVDDCQAWSGRRPLQWLYENVAVDQRWCLVHATHADPAEVAA 280
            A     P+H+H++EQ  E D C+A     P Q L E   +      VHATH D A+V A
Sbjct: 236 EAAR-GRPLHVHLSEQVAENDACRAAYDASPTQVLAEAGVLGPATSAVHATHLDAADVRA 294

Query: 281 MARSGAVAGLCLSTEANLGDGIFPATDFLAQGGRLGIGSDSHVSLSVVEELRWLEYGQRL 340
           +  S   A  C +TE +LGDG+ PA      G  L +GSDSH  + + EE+R +E  +RL
Sbjct: 295 LGTSRTRACFCPTTERDLGDGVGPARALHEAGSALTLGSDSHAVVDLFEEMRAVELDERL 354

Query: 341 RDRKRNRLYRDDQPMIGRTLYDAALAGGAQALGQPIGSLAVGRRADLLVLDGNDPYLASA 400
             R+R           G  L +A L   A       G+L VG RADL+ LD   P  A  
Sbjct: 355 VSRRRGH-------WAGAELLEAGLRHDALGFAD-AGALRVGARADLVTLDTVGPRTAGT 406

Query: 401 EGDALLNRWLFAGGDRQVRDVMVAGRWV 428
             D   +  +FA     V  V+V GR V
Sbjct: 407 GADE--HTAVFAATGADVTQVVVDGRLV 432


Lambda     K      H
   0.321    0.136    0.415 

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: 534
Number of extensions: 31
Number of successful extensions: 5
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: 453
Length of database: 456
Length adjustment: 33
Effective length of query: 420
Effective length of database: 423
Effective search space:   177660
Effective search space used:   177660
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 (21.9 bits)
S2: 51 (24.3 bits)

Align candidate WP_068106976.1 I601_RS04780 (formimidoylglutamate 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.902801.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.3e-131  425.4  12.1   5.8e-131  423.3  12.1    1.7  1  NCBI__GCF_001653335.1:WP_068106976.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001653335.1:WP_068106976.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  423.3  12.1  5.8e-131  5.8e-131       2     431 ..       2     433 ..       1     453 [. 0.89

  Alignments for each domain:
  == domain 1  score: 423.3 bits;  conditional E-value: 5.8e-131
                             TIGR02022   2 kvyfaerallpdgwaegvrlavaedGrilavet........gvsaae.........daerlsgvvlpglanlH 57 
                                           + y +era++ d++ ++v ++++ +Gr ++ve+        g+++++         +++r+ g++lpglan H
  NCBI__GCF_001653335.1:WP_068106976.1   2 SSYLLERAWVEDRVVDDVLVEIE-AGRFTRVEAlggsrrgsGAATPSrlrfprvpgETARVPGLTLPGLANQH 73 
                                           56788888888888888888888.5688888753322221122221111111111145667789********* PP

                             TIGR02022  58 sHAFqralaGlaevagsgaDsFWtWRevmYrlverldPeqleaiarqlyvemlkaGftrvgEFHYlHHaadGt 130
                                           sHAF+ral+G++++ g    +FWtWRe mY l+ rldP++   +a +ly em+  G+t+vgEFHYlHHa+dG 
  NCBI__GCF_001653335.1:WP_068106976.1  74 SHAFHRALRGRTQRGGG---TFWTWREQMYDLAGRLDPDDHLDLATALYREMVAVGITTVGEFHYLHHAPDGR 143
                                           **********9987665...5**************************************************** PP

                             TIGR02022 131 pYadpaelaeriaaAAadaGigltlLpvlYahagFGgaaanegqrrfid.dveaflrlvealrkelaaqeear 202
                                            Ya+p+e +  +++AA+ aG++++lL+++Y ++gFG a+ + +q r+ d d+++++++veal  +  a+++++
  NCBI__GCF_001653335.1:WP_068106976.1 144 AYAEPNETGLVLVEAARRAGLRIALLDTCYLSSGFG-APVEGAQVRYTDgDADRWAQRVEALDAATGADDHVV 215
                                           ************************************.99999******************************* PP

                             TIGR02022 203 lGlaiHslRAvtaeelaavlqaserqlPvHiHvaEqqkEvddClaasgrrPvewLldhaevdarwclvHatHl 275
                                           +G+a+Hs+RAv++++l +v++a+  + P+H+H++Eq +E+d+C+aa    P++ L++ + ++  +++vHatHl
  NCBI__GCF_001653335.1:WP_068106976.1 216 VGAAVHSVRAVPRDQLPTVVEAARGR-PLHVHLSEQVAENDACRAAYDASPTQVLAEAGVLGPATSAVHATHL 287
                                           **********************9998.********************************************** PP

                             TIGR02022 276 tdeevkllaksgavaglCpttEanLgDGifpaadfvaaggrlgiGsDshvvvdvleElRllEygqRLrdraRn 348
                                           ++ +v++l++s++ a+ CpttE++LgDG+ pa ++ +ag+ l++GsDsh+vvd+ eE+R++E+++RL +r+R+
  NCBI__GCF_001653335.1:WP_068106976.1 288 DAADVRALGTSRTRACFCPTTERDLGDGVGPARALHEAGSALTLGSDSHAVVDLFEEMRAVELDERLVSRRRG 360
                                           ************************************************************************* PP

                             TIGR02022 349 vlaageeasvaralydaAlaggaqalGlae.geleaGarADlltldledpslagakgdalldsllfaaekaav 420
                                           ++a       +++l++a l   + alG a+ g+l++GarADl+tld+  p++ag+  d   ++++faa++a+v
  NCBI__GCF_001653335.1:WP_068106976.1 361 HWA-------GAELLEAGLR--HDALGFADaGALRVGARADLVTLDTVGPRTAGTGADE--HTAVFAATGADV 422
                                           **9.......7899998885..7899*98879**********************99997..689********* PP

                             TIGR02022 421 rdvvvaGrkvv 431
                                           ++vvv+Gr v 
  NCBI__GCF_001653335.1:WP_068106976.1 423 TQVVVDGRLVH 433
                                           *******9764 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (455 nodes)
Target sequences:                          1  (456 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.02
# Mc/sec: 7.49
//
[ok]

This GapMind analysis is from Sep 24 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 2024 update 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