Alignments for a candidate for hutF in Dyella japonica UNC79MFTsu3.2

GapMind for catabolism of small carbon sources

Alignments for a candidate for hutF in Dyella japonica UNC79MFTsu3.2

Align formimidoylglutamate deiminase (EC 3.5.3.13) (characterized)
to candidate N515DRAFT_0145 N515DRAFT_0145 formimidoylglutamate deiminase

Query= BRENDA::Q9HU77
         (453 letters)



>FitnessBrowser__Dyella79:N515DRAFT_0145
          Length = 453

 Score =  455 bits (1170), Expect = e-132
 Identities = 247/449 (55%), Positives = 297/449 (66%), Gaps = 10/449 (2%)

Query: 6   AERALLPEGWARNVRFEISADGVLAEIRPDANADGAERLGGAVLPGMPNLHSHAFQRAMA 65
           A++  L +GW+ +  F + A G +A   P+  A   ERLG  VLPGMPNLHSHAFQRAMA
Sbjct: 10  ADQLWLADGWSADGAFAVDASGHVAP--PEGEA---ERLGAWVLPGMPNLHSHAFQRAMA 64

Query: 66  GLAEVAGNPNDSFWTWRELMYRMVARLSPEQIEVIACQLYIEMLKAGYTAVAEFHYVHHD 125
           GLAE  G  +DSFWTWRE MY   A + PE+++ IA QLY+EMLKAGYT V EFHY+HH 
Sbjct: 65  GLAERKGRSDDSFWTWRETMYAFAAAIGPEELKAIAAQLYVEMLKAGYTQVCEFHYLHHQ 124

Query: 126 LDGRSYADPAELSLRISRAASAAGIGLTLLPVLYSHAGFGGQPASEGQRRFINGSEAYLE 185
            DG  YA P  +SL +  AA   GI LTLLPVLY   GF G+P S  QRRF N   +Y+ 
Sbjct: 125 PDGTPYAQPEAMSLALIEAARETGITLTLLPVLYMTGGFDGRPLSARQRRFGNDLSSYVR 184

Query: 186 LLQRLRAPLEAAGHSLGLCFHSLRAVTPQQIATVLAAG-HDDLPVHIHIAEQQKEVDDCQ 244
           LL+ LR   E  G  +G+  HSLRAV  + +  +LA     DLPVHIHIAEQ  EV DC 
Sbjct: 185 LLEALRRH-EGDGLRIGIALHSLRAVPEEAMRGLLATRIAQDLPVHIHIAEQIGEVQDCL 243

Query: 245 AWSGRRPLQWLYENVAVDQRWCLVHATHADPAEVAAMARSGAVAGLCLSTEANLGDGIFP 304
           A  G RP++WL ++  VD RW LVHATH    E + +ARSGAVAGLC +TEANLGDG+FP
Sbjct: 244 ATRGARPVEWLLDHAPVDARWTLVHATHLTGHETSRLARSGAVAGLCPTTEANLGDGLFP 303

Query: 305 ATDFLAQGGRLGIGSDSHVSLSVVEELRWLEYGQRLRDRKRNRLYRDDQPMIGRTLYDAA 364
            +D+L   G LGIGSDSH+S+S VEELRWLEYGQRL  R RN   R +   +G TL+ AA
Sbjct: 304 LSDYLDAKGVLGIGSDSHISISPVEELRWLEYGQRLSTRHRNIAARREGDSVGETLWRAA 363

Query: 365 LAGGAQALGQPIGSLAVGRRADLLVLDGNDPYLASAEGDALLNRWLFAGGDRQVRDVMVA 424
           L GGA+A G P+G L    RADLLVLD   P LA+ +  +LL+ +LFAG    VR VM  
Sbjct: 364 LRGGARAAGLPVGELRAAARADLLVLDDESPLLAARDARSLLDSFLFAGNTPLVRHVMCG 423

Query: 425 GRWVVRDGRH---AGEERSARAFVQVLGE 450
           GRWVVRD RH   AG     RA V+ L +
Sbjct: 424 GRWVVRDFRHHDEAGIAARYRAVVERLAQ 452


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: 637
Number of extensions: 38
Number of successful extensions: 3
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: 453
Length adjustment: 33
Effective length of query: 420
Effective length of database: 420
Effective search space:   176400
Effective search space used:   176400
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 N515DRAFT_0145 N515DRAFT_0145 (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.14282.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
   5.6e-184  598.0   2.0   6.6e-184  597.8   2.0    1.0  1  lcl|FitnessBrowser__Dyella79:N515DRAFT_0145  N515DRAFT_0145 formimidoylglutam


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dyella79:N515DRAFT_0145  N515DRAFT_0145 formimidoylglutamate deiminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  597.8   2.0  6.6e-184  6.6e-184       2     454 ..       6     451 ..       5     452 .. 0.97

  Alignments for each domain:
  == domain 1  score: 597.8 bits;  conditional E-value: 6.6e-184
                                    TIGR02022   2 kvyfaerallpdgwaegvrlavaedGrilavetgvsaaedaerlsgvvlpglanlHsHAFqralaG 67 
                                                  ++y a++++l+dgw+++ ++av+++G+++  e       +aerl+  vlpg++nlHsHAFqra+aG
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0145   6 RTYSADQLWLADGWSADGAFAVDASGHVAPPE------GEAERLGAWVLPGMPNLHSHAFQRAMAG 65 
                                                  67999********************9998873......445899*9******************** PP

                                    TIGR02022  68 laevagsgaDsFWtWRevmYrlverldPeqleaiarqlyvemlkaGftrvgEFHYlHHaadGtpYa 133
                                                  lae++g+++DsFWtWRe mY +++ + Pe+l+aia+qlyvemlkaG+t+v EFHYlHH++dGtpYa
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0145  66 LAERKGRSDDSFWTWRETMYAFAAAIGPEELKAIAAQLYVEMLKAGYTQVCEFHYLHHQPDGTPYA 131
                                                  ****************************************************************** PP

                                    TIGR02022 134 dpaelaeriaaAAadaGigltlLpvlYahagFGgaaanegqrrfiddveaflrlvealrkelaaqe 199
                                                  +p++++ ++++AA+++Gi ltlLpvlY   gF g + +++qrrf +d  +++rl+ealr+  ++ +
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0145 132 QPEAMSLALIEAARETGITLTLLPVLYMTGGFDGRPLSARQRRFGNDLSSYVRLLEALRR--HEGD 195
                                                  ***********************************************************6..4679 PP

                                    TIGR02022 200 earlGlaiHslRAvtaeelaavlq.aserqlPvHiHvaEqqkEvddClaasgrrPvewLldhaevd 264
                                                    r+G+a+HslRAv++e ++ +l+   ++ lPvHiH+aEq  Ev+dCla+ g rPvewLldha+vd
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0145 196 GLRIGIALHSLRAVPEEAMRGLLAtRIAQDLPVHIHIAEQIGEVQDCLATRGARPVEWLLDHAPVD 261
                                                  9********************9984567889*********************************** PP

                                    TIGR02022 265 arwclvHatHltdeevkllaksgavaglCpttEanLgDGifpaadfvaaggrlgiGsDshvvvdvl 330
                                                  arw+lvHatHlt +e+++la+sgavaglCpttEanLgDG+fp +d++ a g lgiGsDsh++++ +
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0145 262 ARWTLVHATHLTGHETSRLARSGAVAGLCPTTEANLGDGLFPLSDYLDAKGVLGIGSDSHISISPV 327
                                                  ****************************************************************** PP

                                    TIGR02022 331 eElRllEygqRLrdraRnvlaageeasvaralydaAlaggaqalGlaegeleaGarADlltldled 396
                                                  eElR+lEygqRL++r Rn  a+ e++sv+++l++aAl gga+a+Gl  gel+a arADll+ld e+
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0145 328 EELRWLEYGQRLSTRHRNIAARREGDSVGETLWRAALRGGARAAGLPVGELRAAARADLLVLDDES 393
                                                  ****************************************************************** PP

                                    TIGR02022 397 pslagakgdalldsllfaaekaavrdvvvaGrkvvrdgrHaleeeierafakvlrall 454
                                                  p la++  ++llds+lfa+++  vr+v+ +Gr+vvrd rH++e+ i+ ++ +v+++l 
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0145 394 PLLAARDARSLLDSFLFAGNTPLVRHVMCGGRWVVRDFRHHDEAGIAARYRAVVERLA 451
                                                  ******************************************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (455 nodes)
Target sequences:                          1  (453 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: 10.75
//
[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