Alignments for a candidate for mmsA in Burkholderia phytofirmans PsJN

GapMind for catabolism of small carbon sources

Alignments for a candidate for mmsA in Burkholderia phytofirmans PsJN

Align malonate-semialdehyde dehydrogenase (EC 1.2.1.15); malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18); methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate BPHYT_RS28825 BPHYT_RS28825 methylmalonate-semialdehyde dehydrogenase

Query= BRENDA::A0A081YAY7
         (498 letters)



>FitnessBrowser__BFirm:BPHYT_RS28825
          Length = 507

 Score =  609 bits (1570), Expect = e-179
 Identities = 306/491 (62%), Positives = 374/491 (76%), Gaps = 4/491 (0%)

Query: 6   HLIGGELIADT-GRTADVFNPSTGEAVRKVPLADRETMQQAIDAAKAAFPAWRNTPPAKR 64
           H IGG   A T GR  DVFNP+TG+    V LA  E +  A+ AA+AAFPAW  T P KR
Sbjct: 17  HYIGGAPAAPTSGRFKDVFNPATGKVTGSVALASVEEVDAAVQAARAAFPAWSETAPLKR 76

Query: 65  AQVLFRFKQLLEANEERIVKLISEEHGKTIEDAAGELKRGIENVEYATAAPEILKGEYSR 124
           A++LFRFK+LL  + + +  LI+ EHGK   DA GE+ RGIE VE+A   P +LK +++ 
Sbjct: 77  ARILFRFKELLNQHHDELAMLITREHGKVFTDAQGEVVRGIEVVEFACGIPNLLKTDFTD 136

Query: 125 NVGPNIDAWSDFQPIGVVAGITPFNFPAMVPLWMYPLAIACGNTFILKPSERDPSSTLLI 184
            +G  ID W+  Q +GVVAGITPFNFP MVP+WM+P+A+ACGNTF+LKPSERDPS++L +
Sbjct: 137 QIGGGIDNWNLRQALGVVAGITPFNFPVMVPMWMFPVALACGNTFVLKPSERDPSASLRL 196

Query: 185 AELFHEAGLPKGVLNVVHGDKGAVDALIEAPEVKALSFVGSTPIAEYIYSEGTKRGKRVQ 244
           AEL  EAGLP GV NVV+GDK AVDALI+ P+V ALSFVGSTPIAEYI++E +KRGKRVQ
Sbjct: 197 AELLKEAGLPDGVFNVVNGDKVAVDALIDHPDVAALSFVGSTPIAEYIHTEASKRGKRVQ 256

Query: 245 ALGGAKNHAVLMPDADLDNAVSALMGAAYGSCGERCMAISVAVCVGDQIADALVQKLVPQ 304
           ALGGAKNH V+MPDADLD AV AL+GAAYGS GERCMAISVAV VG+ +AD L++KLVP+
Sbjct: 257 ALGGAKNHLVVMPDADLDQAVDALIGAAYGSAGERCMAISVAVAVGN-VADKLIEKLVPR 315

Query: 305 IKGLKIGAGTSCGLDMGPLVTGAARDKVTGYIDTGVAQGAELVVDGRGYKVAGHENGFFL 364
           +K L I  G     +MGPLVT   + KVTGYI +G A+GA+L+VDGR + V  +E GFF+
Sbjct: 316 VKSLVIKNGEHLDAEMGPLVTAEHKAKVTGYIASGEAEGAKLIVDGRAHPVT-NEEGFFV 374

Query: 365 GGTLFDRVTPEMTIYKEEIFGPVLCIVRVNSLEEAMQLINDHEYGNGTCIFTRDGEAARL 424
           GGTLFD V  EM IYKEEIFGPVL +VRV     A+ LIN HE+GNG  +FT DG  AR 
Sbjct: 375 GGTLFDHVGTEMKIYKEEIFGPVLAVVRVPDFASAVDLINAHEFGNGVSLFTSDGGVARA 434

Query: 425 FCDEIEVGMVGVNVPLPVPVAYHSFGGWKRSLFGDLHAYGPDGVRFYTKRKAITQRWPQR 484
           F  +I+VGMVG+NVP+PVP+A+HSFGGWKRSLFGD HAYG +GVRFYT+ K+I QRWP  
Sbjct: 435 FGRQIQVGMVGINVPIPVPMAWHSFGGWKRSLFGDHHAYGEEGVRFYTRYKSIMQRWPDS 494

Query: 485 KSHEAAQFAFP 495
            + + A+F  P
Sbjct: 495 IA-KGAEFTMP 504


Lambda     K      H
   0.319    0.137    0.411 

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: 783
Number of extensions: 26
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: 498
Length of database: 507
Length adjustment: 34
Effective length of query: 464
Effective length of database: 473
Effective search space:   219472
Effective search space used:   219472
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 (21.7 bits)
S2: 52 (24.6 bits)

Align candidate BPHYT_RS28825 BPHYT_RS28825 (methylmalonate-semialdehyde dehydrogenase)
to HMM TIGR01722 (mmsA: methylmalonate-semialdehyde dehydrogenase (acylating) (EC 1.2.1.27))

# 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/TIGR01722.hmm
# target sequence database:        /tmp/gapView.1908030.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01722  [M=477]
Accession:   TIGR01722
Description: MMSDH: methylmalonate-semialdehyde dehydrogenase (acylating)
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                -----------
   5.9e-214  697.0   1.0   6.8e-214  696.8   1.0    1.0  1  lcl|FitnessBrowser__BFirm:BPHYT_RS28825  BPHYT_RS28825 methylmalonate-sem


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__BFirm:BPHYT_RS28825  BPHYT_RS28825 methylmalonate-semialdehyde dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  696.8   1.0  6.8e-214  6.8e-214       3     477 .]      17     491 ..      15     491 .. 0.99

  Alignments for each domain:
  == domain 1  score: 696.8 bits;  conditional E-value: 6.8e-214
                                TIGR01722   3 hlidGkfvegksdkyipvsnpatnevlakvaeasaeevdaavasaretfaawaetsvaerarvllryqal 72 
                                              h+i+G+ +  +s+++ +v npat++v++ va as+eevdaav +ar +f+aw+et+ ++rar+l+r+++l
  lcl|FitnessBrowser__BFirm:BPHYT_RS28825  17 HYIGGAPAAPTSGRFKDVFNPATGKVTGSVALASVEEVDAAVQAARAAFPAWSETAPLKRARILFRFKEL 86 
                                              9********************************************************************* PP

                                TIGR01722  73 lkehrdeiaklisaeqGktledakGdvarGlevvehacsvtslllGetvesvakdvdvysirqplGvvaG 142
                                              l++h+de+a li+ e+Gk+++da+G+v+rG+evve+ac+++ ll+ + ++++   +d + +rq lGvvaG
  lcl|FitnessBrowser__BFirm:BPHYT_RS28825  87 LNQHHDELAMLITREHGKVFTDAQGEVVRGIEVVEFACGIPNLLKTDFTDQIGGGIDNWNLRQALGVVAG 156
                                              ********************************************************************** PP

                                TIGR01722 143 itpfnfpamiplwmfplaiacGntfvlkpsekvpsaavklaellseaGapdGvlnvvhGdkeavdrlleh 212
                                              itpfnfp m+p+wmfp+a+acGntfvlkpse++psa+++laell+eaG+pdGv+nvv Gdk+avd l++h
  lcl|FitnessBrowser__BFirm:BPHYT_RS28825 157 ITPFNFPVMVPMWMFPVALACGNTFVLKPSERDPSASLRLAELLKEAGLPDGVFNVVNGDKVAVDALIDH 226
                                              ********************************************************************** PP

                                TIGR01722 213 pdvkavsfvGsvavgeyiyetgsahgkrvqalaGaknhmvvlpdadkeaaldalvgaavGaaGqrcmais 282
                                              pdv a+sfvGs++++eyi++ +s++gkrvqal+Gaknh vv+pdad+++a+dal+gaa+G+aG+rcmais
  lcl|FitnessBrowser__BFirm:BPHYT_RS28825 227 PDVAALSFVGSTPIAEYIHTEASKRGKRVQALGGAKNHLVVMPDADLDQAVDALIGAAYGSAGERCMAIS 296
                                              ********************************************************************** PP

                                TIGR01722 283 aavlvGaa.kelveeireraekvrvgagddpgaelGplitkqakervasliasgakeGaevlldGrgykv 351
                                              +av+vG++ ++l+e+++ r++ + +  g++  ae+Gpl+t ++k++v+ +iasg +eGa++++dGr+  v
  lcl|FitnessBrowser__BFirm:BPHYT_RS28825 297 VAVAVGNVaDKLIEKLVPRVKSLVIKNGEHLDAEMGPLVTAEHKAKVTGYIASGEAEGAKLIVDGRAHPV 366
                                              *******989***********************************************************9 PP

                                TIGR01722 352 eGyeeGnfvGitllervkpdmkiykeeifGpvlvvleadtleeaiklinespyGnGtaiftsdGaaarkf 421
                                                 eeG fvG tl+++v ++mkiykeeifGpvl+v+++  +  a+ lin+  +GnG ++ftsdG+ ar f
  lcl|FitnessBrowser__BFirm:BPHYT_RS28825 367 T-NEEGFFVGGTLFDHVGTEMKIYKEEIFGPVLAVVRVPDFASAVDLINAHEFGNGVSLFTSDGGVARAF 435
                                              7.699***************************************************************** PP

                                TIGR01722 422 qheievGqvGvnvpipvplpffsftGwkdslfGdlhiyGkqGvrfytrlktvtarw 477
                                                +i+vG+vG+nvpipvp++++sf+Gwk slfGd+h+yG++Gvrfytr k +  rw
  lcl|FitnessBrowser__BFirm:BPHYT_RS28825 436 GRQIQVGMVGINVPIPVPMAWHSFGGWKRSLFGDHHAYGEEGVRFYTRYKSIMQRW 491
                                              *******************************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (477 nodes)
Target sequences:                          1  (507 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: 00:00:00.00
# Mc/sec: 27.34
//
[ok]

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

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Protein sequences (fasta format)
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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