Alignments for a candidate for hutF in Stenotrophomonas chelatiphaga DSM 21508

GapMind for catabolism of small carbon sources

Alignments for a candidate for hutF in Stenotrophomonas chelatiphaga DSM 21508

Align formimidoylglutamate deiminase (EC 3.5.3.13) (characterized)
to candidate WP_057506768.1 ABB28_RS00630 formimidoylglutamate deiminase

Query= BRENDA::Q9HU77
         (453 letters)



>NCBI__GCF_001431535.1:WP_057506768.1
          Length = 456

 Score =  451 bits (1161), Expect = e-131
 Identities = 239/451 (52%), Positives = 294/451 (65%), Gaps = 5/451 (1%)

Query: 3   AIFAERALLPEGWARNVRFEISADGVLAEIRPDANADGAERLGGAVLPGMPNLHSHAFQR 62
           A  A RALLP+GWAR+VR  +  DG + EI         ++    ++PG+PNLHSHAFQR
Sbjct: 9   AFHAARALLPQGWARDVRLTVD-DGCIGEIHVGVPTQAGDQGVQILVPGVPNLHSHAFQR 67

Query: 63  AMAGLAEVAGNPNDSFWTWRELMYRMVARLSPEQIEVIACQLYIEMLKAGYTAVAEFHYV 122
            MAGL E+ G   DSFW+WRELMYR +ARL PE +E IA Q Y+EML++G+T V EFHY+
Sbjct: 68  GMAGLTEIGGGDGDSFWSWRELMYRFLARLVPEAVEAIAAQAYMEMLESGFTRVGEFHYL 127

Query: 123 HHDLDGRSYADPAELSLRISRAASAAGIGLTLLPVLYSHAGFGGQPASEGQRRFINGSEA 182
           HHD DGR YAD AE+S RI+ AA+  GIGLTLLPV Y+HA FGG   +  QRR I+  + 
Sbjct: 128 HHDADGRPYADRAEMSARIAAAAAQTGIGLTLLPVFYAHADFGGAAPNPAQRRLIHDVDG 187

Query: 183 YLELLQRLRAPLEAAGHS-LGLCFHSLRAVTPQQIATVLAAGHDDLPVHIHIAEQQKEVD 241
           + +LL   R  L     + LG+  HSLRAVT ++++ +L    +D PVHIHIAEQ +EVD
Sbjct: 188 FAQLLDGARTALRVLPDAVLGIAPHSLRAVTGEELSALLPL--NDGPVHIHIAEQLREVD 245

Query: 242 DCQAWSGRRPLQWLYENVAVDQRWCLVHATHADPAEVAAMARSGAVAGLCLSTEANLGDG 301
            C  WSG RP++WLYEN AVD RWCLVHATH D  E A +  S AVAGLC  TEANLGDG
Sbjct: 246 ACVGWSGLRPVRWLYENAAVDARWCLVHATHIDDDERARIVASHAVAGLCPITEANLGDG 305

Query: 302 IFPATDFLAQGGRLGIGSDSHVSLSVVEELRWLEYGQRLRDRKRNRLYRDDQPMIGRTLY 361
           +FP   F  +GGR GIGSDS+V +   EELR LEYGQRL  R RN +  D Q   GR L+
Sbjct: 306 LFPMQAFAREGGRFGIGSDSNVLIDAAEELRLLEYGQRLSLRGRNVIAPDAQRSSGRFLF 365

Query: 362 DAALAGGAQALGQPIGSLAVGRRADLLVLDGNDPYLASAEGDALLNRWLFAGGDRQVRDV 421
           D A  GGAQALG  +  L  G  ADLL LD   P + + +GDALL+ W+FA  +  +R  
Sbjct: 366 DGAQHGGAQALG-VLAGLQPGASADLLELDAGHPAMLARDGDALLDSWVFAARNGALRSA 424

Query: 422 MVAGRWVVRDGRHAGEERSARAFVQVLGELL 452
              GR  V DGRH   +     F Q L  +L
Sbjct: 425 WRRGRQCVADGRHLQRDAITARFAQALRGVL 455


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: 695
Number of extensions: 33
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_057506768.1 ABB28_RS00630 (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.12923.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
     5e-199  647.6   2.3   5.6e-199  647.5   2.3    1.0  1  lcl|NCBI__GCF_001431535.1:WP_057506768.1  ABB28_RS00630 formimidoylglutama


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_001431535.1:WP_057506768.1  ABB28_RS00630 formimidoylglutamate deiminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  647.5   2.3  5.6e-199  5.6e-199       3     453 ..       9     454 ..       7     456 .] 0.98

  Alignments for each domain:
  == domain 1  score: 647.5 bits;  conditional E-value: 5.6e-199
                                 TIGR02022   3 vyfaerallpdgwaegvrlavaedGrilavetgvsaaedaerlsgvvlpglanlHsHAFqralaGlaev 71 
                                               +++a+rallp+gwa++vrl+v+ dG i  ++ gv++  +++ ++ +++pg++nlHsHAFqr++aGl+e 
  lcl|NCBI__GCF_001431535.1:WP_057506768.1   9 AFHAARALLPQGWARDVRLTVD-DGCIGEIHVGVPTQAGDQGVQ-ILVPGVPNLHSHAFQRGMAGLTEI 75 
                                               6899*****************9.78**********988888888.9*********************** PP

                                 TIGR02022  72 agsgaDsFWtWRevmYrlverldPeqleaiarqlyvemlkaGftrvgEFHYlHHaadGtpYadpaelae 140
                                                g  +DsFW+WRe+mYr+++rl Pe +eaia+q+y+eml++GftrvgEFHYlHH+adG pYad+ae+++
  lcl|NCBI__GCF_001431535.1:WP_057506768.1  76 GGGDGDSFWSWRELMYRFLARLVPEAVEAIAAQAYMEMLESGFTRVGEFHYLHHDADGRPYADRAEMSA 144
                                               ********************************************************************* PP

                                 TIGR02022 141 riaaAAadaGigltlLpvlYahagFGgaaanegqrrfiddveaflrlvealrkelaaqeearlGlaiHs 209
                                               riaaAAa++GigltlLpv+Yaha+FGgaa+n++qrr+i+dv+ f++l++  r++l+  ++a+lG+a+Hs
  lcl|NCBI__GCF_001431535.1:WP_057506768.1 145 RIAAAAAQTGIGLTLLPVFYAHADFGGAAPNPAQRRLIHDVDGFAQLLDGARTALRVLPDAVLGIAPHS 213
                                               ********************************************************************* PP

                                 TIGR02022 210 lRAvtaeelaavlqaserqlPvHiHvaEqqkEvddClaasgrrPvewLldhaevdarwclvHatHltde 278
                                               lRAvt eel+a+l++++   PvHiH+aEq +Evd+C+ +sg rPv+wL+++a vdarwclvHatH++d+
  lcl|NCBI__GCF_001431535.1:WP_057506768.1 214 LRAVTGEELSALLPLNDG--PVHIHIAEQLREVDACVGWSGLRPVRWLYENAAVDARWCLVHATHIDDD 280
                                               ***************998..************************************************* PP

                                 TIGR02022 279 evkllaksgavaglCpttEanLgDGifpaadfvaaggrlgiGsDshvvvdvleElRllEygqRLrdraR 347
                                               e ++++ s+avaglCp+tEanLgDG+fp+++f+++ggr+giGsDs+v++d++eElRllEygqRL+ r R
  lcl|NCBI__GCF_001431535.1:WP_057506768.1 281 ERARIVASHAVAGLCPITEANLGDGLFPMQAFAREGGRFGIGSDSNVLIDAAEELRLLEYGQRLSLRGR 349
                                               ********************************************************************* PP

                                 TIGR02022 348 nvlaageeasvaralydaAlaggaqalGlaegeleaGarADlltldledpslagakgdalldsllfaae 416
                                               nv+a + ++s++r l+d A  ggaqalG  + +l+ Ga+ADll+ld+ +p+++++ gdallds++faa+
  lcl|NCBI__GCF_001431535.1:WP_057506768.1 350 NVIAPDAQRSSGRFLFDGAQHGGAQALGVLA-GLQPGASADLLELDAGHPAMLARDGDALLDSWVFAAR 417
                                               ****************************975.7************************************ PP

                                 TIGR02022 417 kaavrdvvvaGrkvvrdgrHaleeeierafakvlral 453
                                               + a+r  +++Gr+ v dgrH ++++i+ +fa++lr +
  lcl|NCBI__GCF_001431535.1:WP_057506768.1 418 NGALRSAWRRGRQCVADGRHLQRDAITARFAQALRGV 454
                                               *********************************9865 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: 7.71
//
[ok]

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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