Alignments for a candidate for astE in Burkholderia phytofirmans PsJN

GapMind for catabolism of small carbon sources

Alignments for a candidate for astE in Burkholderia phytofirmans PsJN

Align Succinylglutamate desuccinylase (EC 3.5.1.96) (characterized)
to candidate BPHYT_RS07720 BPHYT_RS07720 succinylglutamate desuccinylase

Query= reanno::BFirm:BPHYT_RS07720
         (342 letters)



>FitnessBrowser__BFirm:BPHYT_RS07720
          Length = 342

 Score =  683 bits (1762), Expect = 0.0
 Identities = 342/342 (100%), Positives = 342/342 (100%)

Query: 1   MPVPLLDDFLAYTLAGTRPAASETQGTCAGGVRWSWLDDGVLLMEPAAQDESVRSVLVSA 60
           MPVPLLDDFLAYTLAGTRPAASETQGTCAGGVRWSWLDDGVLLMEPAAQDESVRSVLVSA
Sbjct: 1   MPVPLLDDFLAYTLAGTRPAASETQGTCAGGVRWSWLDDGVLLMEPAAQDESVRSVLVSA 60

Query: 61  GVHGDETAPIELLGFLVRDIAQGTAALTCRLLVILGNVDAMRDACRYRDDDLNRLFSGRH 120
           GVHGDETAPIELLGFLVRDIAQGTAALTCRLLVILGNVDAMRDACRYRDDDLNRLFSGRH
Sbjct: 61  GVHGDETAPIELLGFLVRDIAQGTAALTCRLLVILGNVDAMRDACRYRDDDLNRLFSGRH 120

Query: 121 LQVPQSYEAPRAAALEQAATQFFAAASNKSGARWHIDMHTAIRASAFEQFALLPHTGKPF 180
           LQVPQSYEAPRAAALEQAATQFFAAASNKSGARWHIDMHTAIRASAFEQFALLPHTGKPF
Sbjct: 121 LQVPQSYEAPRAAALEQAATQFFAAASNKSGARWHIDMHTAIRASAFEQFALLPHTGKPF 180

Query: 181 SRAMFEWLGEARISAVLLHTTKGNTYSHFTAQVCGAEACTLELGKVRPFGQNDLTRFAGA 240
           SRAMFEWLGEARISAVLLHTTKGNTYSHFTAQVCGAEACTLELGKVRPFGQNDLTRFAGA
Sbjct: 181 SRAMFEWLGEARISAVLLHTTKGNTYSHFTAQVCGAEACTLELGKVRPFGQNDLTRFAGA 240

Query: 241 DHAVRHLLAGMRGHVRADLPRAFTVIDQITKQSDAFELLVAADVANFTPFAKGTVLARDG 300
           DHAVRHLLAGMRGHVRADLPRAFTVIDQITKQSDAFELLVAADVANFTPFAKGTVLARDG
Sbjct: 241 DHAVRHLLAGMRGHVRADLPRAFTVIDQITKQSDAFELLVAADVANFTPFAKGTVLARDG 300

Query: 301 EYRYVVQHDEERLVFPNATVKPGLRAGLMVVETTQDTLSKLV 342
           EYRYVVQHDEERLVFPNATVKPGLRAGLMVVETTQDTLSKLV
Sbjct: 301 EYRYVVQHDEERLVFPNATVKPGLRAGLMVVETTQDTLSKLV 342


Lambda     K      H
   0.322    0.135    0.403 

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: 513
Number of extensions: 7
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: 342
Length of database: 342
Length adjustment: 29
Effective length of query: 313
Effective length of database: 313
Effective search space:    97969
Effective search space used:    97969
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: 49 (23.5 bits)

Align candidate BPHYT_RS07720 BPHYT_RS07720 (succinylglutamate desuccinylase)
to HMM TIGR03242 (astE: succinylglutamate desuccinylase (EC 3.5.1.96))

# 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/TIGR03242.hmm
# target sequence database:        /tmp/gapView.26075.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR03242  [M=319]
Accession:   TIGR03242
Description: arg_catab_astE: succinylglutamate desuccinylase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                -----------
   5.2e-131  422.6   0.0   5.9e-131  422.5   0.0    1.0  1  lcl|FitnessBrowser__BFirm:BPHYT_RS07720  BPHYT_RS07720 succinylglutamate 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__BFirm:BPHYT_RS07720  BPHYT_RS07720 succinylglutamate desuccinylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  422.5   0.0  5.9e-131  5.9e-131       1     319 []       8     331 ..       8     331 .. 0.96

  Alignments for each domain:
  == domain 1  score: 422.5 bits;  conditional E-value: 5.9e-131
                                TIGR03242   1 dflaltlekkepevtqge...aknvklrwldeGvlelePe..aeaekslvisaGihGnetaPielleqll 65 
                                              dfla tl+  +p + +++   a +v++ wld+Gvl +eP+  +e  +s+++saG+hG+etaPiell  l+
  lcl|FitnessBrowser__BFirm:BPHYT_RS07720   8 DFLAYTLAGTRPAASETQgtcAGGVRWSWLDDGVLLMEPAaqDESVRSVLVSAGVHGDETAPIELLGFLV 77 
                                              79******9999655444347889***************96667789*********************** PP

                                TIGR03242  66 sdiaagklqlkvrlLlilGnpaalrkgkRyleedlnRlfgGryqeleeskeklRaeeLeqvveaffeagk 135
                                              +dia+g+ +l +rlL+ilGn  a+r + Ry ++dlnRlf+Gr+ ++ +s e+ Ra+ Leq++++ff+a++
  lcl|FitnessBrowser__BFirm:BPHYT_RS07720  78 RDIAQGTAALTCRLLVILGNVDAMRDACRYRDDDLNRLFSGRHLQVPQSYEAPRAAALEQAATQFFAAAS 147
                                              ******************************************************************9876 PP

                                TIGR03242 136 a.searyhyDlhtaiRasklekfallPyqekpfdkellewlaaadldavllhkekggtfshfssekleae 204
                                              + s ar+h+D+htaiRas +e+fallP+++kpf+++++ewl++a + avllh++kg+t+shf+++ ++ae
  lcl|FitnessBrowser__BFirm:BPHYT_RS07720 148 NkSGARWHIDMHTAIRASAFEQFALLPHTGKPFSRAMFEWLGEARISAVLLHTTKGNTYSHFTAQVCGAE 217
                                              61556***************************************************************** PP

                                TIGR03242 205 actlelGkarPfGendlsqfqaitealralisdeaiparkkeelklfevvesilkksdsfelhvaedasn 274
                                              actlelGk+rPfG+ndl++f+ +++a+r l+++ +   r   + ++f+v+++i+k+sd+fel va+d+ n
  lcl|FitnessBrowser__BFirm:BPHYT_RS07720 218 ACTLELGKVRPFGQNDLTRFAGADHAVRHLLAGMRGHVRADLP-RAFTVIDQITKQSDAFELLVAADVAN 286
                                              *********************************9999999989.9************************* PP

                                TIGR03242 275 ftefakGtllaedkderyrveeeeerilfPnakvanGlRaglllv 319
                                              ft+fakGt+la+d ++ry+v+++eer++fPna+v+ GlRagl++v
  lcl|FitnessBrowser__BFirm:BPHYT_RS07720 287 FTPFAKGTVLARDGEYRYVVQHDEERLVFPNATVKPGLRAGLMVV 331
                                              *******************************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (319 nodes)
Target sequences:                          1  (342 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 7.21
//
[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