Alignments for a candidate for hutG in Paraburkholderia bryophila 376MFSha3.1

GapMind for catabolism of small carbon sources

Alignments for a candidate for hutG in Paraburkholderia bryophila 376MFSha3.1

Align Formiminoglutamase (EC 3.5.3.8) (characterized)
to candidate H281DRAFT_03347 H281DRAFT_03347 formiminoglutamase

Query= reanno::Koxy:BWI76_RS08725
         (318 letters)



>FitnessBrowser__Burk376:H281DRAFT_03347
          Length = 322

 Score =  217 bits (553), Expect = 3e-61
 Identities = 132/321 (41%), Positives = 178/321 (55%), Gaps = 16/321 (4%)

Query: 6   PTPAALWQGRDDSAEAANALRLFQTIVRAERFEPEMLAGDI-ALLGFACDEGVRRNKGRT 64
           P    +W GR D  E  +  R+F  +        + +  D+  ++GF+ DEGVRRN+GR 
Sbjct: 4   PFDGKVWAGRSDDGEPGDTRRVFNQVTPFG--SAQQVQRDVPVIVGFSSDEGVRRNQGRI 61

Query: 65  GAERGPETLRRALANMASHDGHDRCVDMGTIHVADDALEAAQQALREAVTACQRAGKRTL 124
           GA   P+ LRR LA + +        D G +   D  LEAAQ  L   V+    +G R L
Sbjct: 62  GAAHAPKELRRVLAGLPAKAAIAALADAGDVVCDDGDLEAAQAELAHVVSEVLASGARPL 121

Query: 125 VLGGGHETAFGHGAGVLDAFPGEEVG------------IINLDAHLDLRIADRASSGTPF 172
           V GGGHE A+G  +G L      E G            IIN DAH DLR    A+SGTPF
Sbjct: 122 VFGGGHEVAWGTYSG-LRLHQQREAGNQATLLISRKLLIINFDAHFDLRQKRPANSGTPF 180

Query: 173 RQLALACEAQRRAFHYACIGVSRAANTQALLDEAARRGVTIIEDLDVLNAFEARAIPELA 232
            Q+AL CE +  +F+Y C G+S   NT +L   A R GV  + D+D+      + + EL 
Sbjct: 181 DQIALDCEERGVSFNYVCFGISDLGNTASLFAHAERLGVRYVLDVDMQETQLPQRLNELQ 240

Query: 233 RNIARYDRLYLTIDLDVLPAREMPAVSAPAALGIPLATLLRIVEPLCRSGKLQAVDLVEF 292
           + +   D +YLTIDLDVLPA   P VSAPAALG+PL+ +  +V  +  SGKL+A D+ E+
Sbjct: 241 KLLDAADDVYLTIDLDVLPAATAPGVSAPAALGVPLSVVEAMVLRVRASGKLRASDIAEY 300

Query: 293 NPQYDIDSQGARAAARLAWQI 313
           NP  D D + ARAAARLA+++
Sbjct: 301 NPTLDQDRRTARAAARLAYRL 321


Lambda     K      H
   0.322    0.135    0.408 

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: 268
Number of extensions: 14
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: 318
Length of database: 322
Length adjustment: 28
Effective length of query: 290
Effective length of database: 294
Effective search space:    85260
Effective search space used:    85260
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: 48 (23.1 bits)

Align candidate H281DRAFT_03347 H281DRAFT_03347 (formiminoglutamase)
to HMM TIGR01227 (hutG: formimidoylglutamase (EC 3.5.3.8))

# 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/TIGR01227.hmm
# target sequence database:        /tmp/gapView.28419.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01227  [M=307]
Accession:   TIGR01227
Description: hutG: formimidoylglutamase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
    2.7e-94  301.8   0.1    3.1e-94  301.6   0.1    1.0  1  lcl|FitnessBrowser__Burk376:H281DRAFT_03347  H281DRAFT_03347 formiminoglutama


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Burk376:H281DRAFT_03347  H281DRAFT_03347 formiminoglutamase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  301.6   0.1   3.1e-94   3.1e-94       1     304 [.      10     320 ..      10     322 .] 0.93

  Alignments for each domain:
  == domain 1  score: 301.6 bits;  conditional E-value: 3.1e-94
                                    TIGR01227   1 lqgrldleeaskkrrdeqvakvvdlveledaqdekgvaliGvaldkgvirnkGrtGAkeaPsairq 66 
                                                  + gr d  e ++ rr+++ +++       ++ +   ++++G+ +d+gv+rn+Gr+GA +aP+ +r+
  lcl|FitnessBrowser__Burk376:H281DRAFT_03347  10 WAGRSDDGEPGDTRRVFNQVTPFGSA---QQVQRDVPVIVGFSSDEGVRRNQGRIGAAHAPKELRR 72 
                                                  78889999999999998888888773...44677889***************************** PP

                                    TIGR01227  67 alanlgdlvasealyDlGdivlegddlvdaqkevaqavaelladarvvvllGGdneiayatikala 132
                                                   la+l++  a  al+D+Gd+v++++dl++aq+e+a++v e+la+++++++ GG++e+a+ t+ +l+
  lcl|FitnessBrowser__Burk376:H281DRAFT_03347  73 VLAGLPAKAAIAALADAGDVVCDDGDLEAAQAELAHVVSEVLASGARPLVFGGGHEVAWGTYSGLR 138
                                                  *****************************************************************9 PP

                                    TIGR01227 133 qa...akgek..........riGvinfDAHfDlRavederptsGTpfrqlldeeqaed..fhlivl 183
                                                   +                  +  +infDAHfDlR+     + sGTpf q++  +++ +  f++++ 
  lcl|FitnessBrowser__Burk376:H281DRAFT_03347 139 LHqqrE---AgnqatllisrKLLIINFDAHFDLRQKR--PANSGTPFDQIALDCEERGvsFNYVCF 199
                                                  985332...22446677776677***********998..999****************99****** PP

                                    TIGR01227 184 GirrfsntqalfdyakkkgvryvtddalaelsletikdileefldevDfiyltvdlDVldaasAPG 249
                                                  Gi+ ++nt++lf++a+++gvryv+d  ++e++l++ ++ l+++ld  D +ylt+dlDVl+aa APG
  lcl|FitnessBrowser__Burk376:H281DRAFT_03347 200 GISDLGNTASLFAHAERLGVRYVLDVDMQETQLPQRLNELQKLLDAADDVYLTIDLDVLPAATAPG 265
                                                  ****************************************************************** PP

                                    TIGR01227 250 vsApaagGleleellelvkriaasdkvrgveivEvnPtlDaddrTarlaArlvah 304
                                                  vsApaa G+ l++++++v r+ as+k+r  +i+E+nPtlD d rTar+aArl   
  lcl|FitnessBrowser__Burk376:H281DRAFT_03347 266 VSAPAALGVPLSVVEAMVLRVRASGKLRASDIAEYNPTLDQDRRTARAAARLAYR 320
                                                  ***************************************************9765 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (307 nodes)
Target sequences:                          1  (322 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: 7.58
//
[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