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_RS21100 BPHYT_RS21100 methylmalonate-semialdehyde dehydrogenase

Query= BRENDA::A0A081YAY7
         (498 letters)



>FitnessBrowser__BFirm:BPHYT_RS21100
          Length = 501

 Score =  617 bits (1592), Expect = 0.0
 Identities = 297/497 (59%), Positives = 378/497 (76%), Gaps = 4/497 (0%)

Query: 4   IKHLIGGELIAD--TGRTADVFNPSTGEAVRKVPLADRETMQQAIDAAKAAFPAWRNTPP 61
           I H I G+  A      T  VFNP+ GEAV +V +   E +  A+ AA AAFPAW   PP
Sbjct: 7   ISHFINGQRTASLRNAETQAVFNPALGEAVAQVAMGSAEDIHAAVGAAAAAFPAWSARPP 66

Query: 62  AKRAQVLFRFKQLLEANEERIVKLISEEHGKTIEDAAGELKRGIENVEYATAAPEILKGE 121
             RA++L ++ QL++ + + + ++++ EHGKT++DA GE+ RG+E VE+A   P +LKGE
Sbjct: 67  LARARILAKYLQLMQQHTDTLAQMLTREHGKTLDDARGEVARGLEVVEFAVGIPHLLKGE 126

Query: 122 YSRNVGPNIDAWSDFQPIGVVAGITPFNFPAMVPLWMYPLAIACGNTFILKPSERDPSST 181
           +S  +   IDAWS  QP+GVVAGITPFNFPAMVP+WM+P+A+ACGNTF+LKPSERDPS +
Sbjct: 127 FSDQISRGIDAWSIRQPLGVVAGITPFNFPAMVPMWMFPIALACGNTFVLKPSERDPSCS 186

Query: 182 LLIAELFHEAGLPKGVLNVVHGDKGAVDALIEAPEVKALSFVGSTPIAEYIYSEGTKRGK 241
           LL AEL  EAGLP GV NVV GDK  VDAL++ PEV+A+SFVGSTPIAEY+Y+  +  GK
Sbjct: 187 LLHAELLKEAGLPDGVFNVVQGDKAVVDALLDHPEVQAVSFVGSTPIAEYVYARASANGK 246

Query: 242 RVQALGGAKNHAVLMPDADLDNAVSALMGAAYGSCGERCMAISVAVCVGDQIADALVQKL 301
           R QALGGAKNH V+MPDAD+  A  AL+GAA+GS GERCMAISVAV VGD + D LV  L
Sbjct: 247 RAQALGGAKNHLVVMPDADMAMATDALIGAAFGSAGERCMAISVAVAVGD-VGDRLVAAL 305

Query: 302 VPQIKGLKIGAGTSCGLDMGPLVTGAARDKVTGYIDTGVAQGAELVVDGRGYKVAGHENG 361
             + + LKI  GT+ G +MGP++T AAR+++   I  GVA GA LVVDGR Y+V G E+G
Sbjct: 306 AERTRALKIDDGTAPGAEMGPVITAAARERIESLIGAGVADGATLVVDGRDYRVPGRESG 365

Query: 362 FFLGGTLFDRVTPEMTIYKEEIFGPVLCIVRVNSLEEAMQLINDHEYGNGTCIFTRDGEA 421
           FF+GGTLFD VTPEMT+Y+EEIFGPVLC+VRV ++  A++LIN HEYGNG  +FTRDG  
Sbjct: 366 FFVGGTLFDHVTPEMTVYREEIFGPVLCVVRVPNVAAAVELINAHEYGNGVAVFTRDGGV 425

Query: 422 ARLFCDEIEVGMVGVNVPLPVPVAYHSFGGWKRSLFGDLHAYGPDGVRFYTKRKAITQRW 481
           AR F  ++++GMVGVNVP+PVP+A++SFGGWKRSLFGD H YGP+GVRFYT+ KA+ QRW
Sbjct: 426 AREFTRQVQIGMVGVNVPVPVPMAFNSFGGWKRSLFGDHHIYGPEGVRFYTRHKAVMQRW 485

Query: 482 PQRKSHEAAQFAFPSNS 498
           P   +   A+FAFP ++
Sbjct: 486 PDTIT-AGAEFAFPQHN 501


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: 758
Number of extensions: 30
Number of successful extensions: 2
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: 501
Length adjustment: 34
Effective length of query: 464
Effective length of database: 467
Effective search space:   216688
Effective search space used:   216688
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_RS21100 BPHYT_RS21100 (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.5664.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                -----------
   1.4e-210  685.9   1.5   1.6e-210  685.7   1.5    1.0  1  lcl|FitnessBrowser__BFirm:BPHYT_RS21100  BPHYT_RS21100 methylmalonate-sem


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__BFirm:BPHYT_RS21100  BPHYT_RS21100 methylmalonate-semialdehyde dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  685.7   1.5  1.6e-210  1.6e-210       2     477 .]       8     485 ..       7     485 .. 0.99

  Alignments for each domain:
  == domain 1  score: 685.7 bits;  conditional E-value: 1.6e-210
                                TIGR01722   2 khlidGkfveg.ksdkyipvsnpatnevlakvaeasaeevdaavasaretfaawaetsvaerarvllryq 70 
                                               h+i+G+   + ++++   v npa +e +a+va+ sae+++aav +a  +f+aw+  + + rar+l +y 
  lcl|FitnessBrowser__BFirm:BPHYT_RS21100   8 SHFINGQRTASlRNAETQAVFNPALGEAVAQVAMGSAEDIHAAVGAAAAAFPAWSARPPLARARILAKYL 77 
                                              79***98776615678889*************************************************** PP

                                TIGR01722  71 allkehrdeiaklisaeqGktledakGdvarGlevvehacsvtslllGetvesvakdvdvysirqplGvv 140
                                              +l+++h d +a++++ e+Gktl+da+G+varGlevve+a +++ ll+Ge ++++++ +d +sirqplGvv
  lcl|FitnessBrowser__BFirm:BPHYT_RS21100  78 QLMQQHTDTLAQMLTREHGKTLDDARGEVARGLEVVEFAVGIPHLLKGEFSDQISRGIDAWSIRQPLGVV 147
                                              ********************************************************************** PP

                                TIGR01722 141 aGitpfnfpamiplwmfplaiacGntfvlkpsekvpsaavklaellseaGapdGvlnvvhGdkeavdrll 210
                                              aGitpfnfpam+p+wmfp+a+acGntfvlkpse++ps+++  aell+eaG+pdGv+nvv Gdk  vd ll
  lcl|FitnessBrowser__BFirm:BPHYT_RS21100 148 AGITPFNFPAMVPMWMFPIALACGNTFVLKPSERDPSCSLLHAELLKEAGLPDGVFNVVQGDKAVVDALL 217
                                              ********************************************************************** PP

                                TIGR01722 211 ehpdvkavsfvGsvavgeyiyetgsahgkrvqalaGaknhmvvlpdadkeaaldalvgaavGaaGqrcma 280
                                              +hp+v+avsfvGs++++ey+y ++sa+gkr qal+Gaknh vv+pdad + a dal+gaa+G+aG+rcma
  lcl|FitnessBrowser__BFirm:BPHYT_RS21100 218 DHPEVQAVSFVGSTPIAEYVYARASANGKRAQALGGAKNHLVVMPDADMAMATDALIGAAFGSAGERCMA 287
                                              ********************************************************************** PP

                                TIGR01722 281 isaavlvGaa.kelveeireraekvrvgagddpgaelGplitkqakervasliasgakeGaevlldGrgy 349
                                              is+av+vG++ ++lv  + er + ++++ g+ pgae+Gp+it +a+er++sli++g+++Ga +++dGr y
  lcl|FitnessBrowser__BFirm:BPHYT_RS21100 288 ISVAVAVGDVgDRLVAALAERTRALKIDDGTAPGAEMGPVITAAARERIESLIGAGVADGATLVVDGRDY 357
                                              **********99********************************************************** PP

                                TIGR01722 350 kveGyeeGnfvGitllervkpdmkiykeeifGpvlvvleadtleeaiklinespyGnGtaiftsdGaaar 419
                                              +v G e G fvG tl+++v p+m++y+eeifGpvl+v+++  +  a++lin+  yGnG a+ft+dG+ ar
  lcl|FitnessBrowser__BFirm:BPHYT_RS21100 358 RVPGRESGFFVGGTLFDHVTPEMTVYREEIFGPVLCVVRVPNVAAAVELINAHEYGNGVAVFTRDGGVAR 427
                                              ********************************************************************** PP

                                TIGR01722 420 kfqheievGqvGvnvpipvplpffsftGwkdslfGdlhiyGkqGvrfytrlktvtarw 477
                                              +f  ++++G+vGvnvp+pvp++f sf+Gwk slfGd+hiyG +Gvrfytr k+v  rw
  lcl|FitnessBrowser__BFirm:BPHYT_RS21100 428 EFTRQVQIGMVGVNVPVPVPMAFNSFGGWKRSLFGDHHIYGPEGVRFYTRHKAVMQRW 485
                                              *********************************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (477 nodes)
Target sequences:                          1  (501 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 9.73
//
[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