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_RS19500 BPHYT_RS19500 methylmalonate-semialdehyde dehydrogenase

Query= BRENDA::A0A081YAY7
         (498 letters)



>FitnessBrowser__BFirm:BPHYT_RS19500
          Length = 512

 Score =  628 bits (1619), Expect = 0.0
 Identities = 309/493 (62%), Positives = 377/493 (76%), Gaps = 3/493 (0%)

Query: 4   IKHLIGGELIADT-GRTADVFNPSTGEAVRKVPLADRETMQQAIDAAKAAFPAWRNTPPA 62
           + H I G+    T GR  DVFNP+ G    +VPLA    +  A+ AAKAAFPAW  T P 
Sbjct: 19  LTHFINGKTFEGTSGRFGDVFNPAQGSVSARVPLASVAEVDAAVAAAKAAFPAWSETAPI 78

Query: 63  KRAQVLFRFKQLLEANEERIVKLISEEHGKTIEDAAGELKRGIENVEYATAAPEILKGEY 122
           KRA+VLF+FK+LL+ + + + +LI+ EHGK   DA GE+ RGIE VE+A   P +LK ++
Sbjct: 79  KRARVLFKFKELLDRHHDELAELITREHGKVFSDAKGEVMRGIEIVEFACGIPNLLKTDF 138

Query: 123 SRNVGPNIDAWSDFQPIGVVAGITPFNFPAMVPLWMYPLAIACGNTFILKPSERDPSSTL 182
           +  +G  ID W+  QP+GVVAGITPFNFP MVP WM+P+AIACGNTF+LKPSERDPS + 
Sbjct: 139 TDQIGGGIDNWNLRQPLGVVAGITPFNFPMMVPCWMFPVAIACGNTFVLKPSERDPSCSN 198

Query: 183 LIAELFHEAGLPKGVLNVVHGDKGAVDALIEAPEVKALSFVGSTPIAEYIYSEGTKRGKR 242
            +AEL  EAGLP GV NVVHGDK AVDAL+  PEV ALSFVGSTPIAEYIY+EGTK GKR
Sbjct: 199 RLAELLKEAGLPDGVFNVVHGDKVAVDALLVHPEVSALSFVGSTPIAEYIYTEGTKHGKR 258

Query: 243 VQALGGAKNHAVLMPDADLDNAVSALMGAAYGSCGERCMAISVAVCVGDQIADALVQKLV 302
           VQALGGAKNH V+MPDADLD AV AL+GAAYGS GERCMAISVAV VG  IAD L+++L 
Sbjct: 259 VQALGGAKNHLVVMPDADLDQAVDALIGAAYGSAGERCMAISVAVAVG-HIADELIERLT 317

Query: 303 PQIKGLKIGAGTSCGLDMGPLVTGAARDKVTGYIDTGVAQGAELVVDGRGYKVAGHENGF 362
           P++K LKI  G     +MGPLVT   R+KV GYID+GV  GA+LVVDGRG++V+GHE GF
Sbjct: 318 PRVKSLKILNGMESDAEMGPLVTAVHREKVVGYIDSGVEAGAKLVVDGRGHQVSGHEKGF 377

Query: 363 FLGGTLFDRVTPEMTIYKEEIFGPVLCIVRVNSLEEAMQLINDHEYGNGTCIFTRDGEAA 422
           FLGGTLFD V+ +M IY+EEIFGPVLC+VRV     A++LIN +E+ NG  +FT DG  A
Sbjct: 378 FLGGTLFDNVSTDMKIYREEIFGPVLCVVRVPDFASAVELINANEFANGVSLFTSDGGVA 437

Query: 423 RLFCDEIEVGMVGVNVPLPVPVAYHSFGGWKRSLFGDLHAYGPDGVRFYTKRKAITQRWP 482
           R F  +I++GMVG+NVP+PVP+A+HSFGGWK+SLFGD HAYG +GVRFYT+ K+I QRWP
Sbjct: 438 RAFSRQIQIGMVGINVPIPVPMAWHSFGGWKKSLFGDHHAYGEEGVRFYTRYKSIMQRWP 497

Query: 483 QRKSHEAAQFAFP 495
              + + A+F  P
Sbjct: 498 DSIA-KGAEFTMP 509


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: 779
Number of extensions: 25
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: 512
Length adjustment: 34
Effective length of query: 464
Effective length of database: 478
Effective search space:   221792
Effective search space used:   221792
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_RS19500 BPHYT_RS19500 (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.17474.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                -----------
   1.1e-223  729.2   0.3   1.2e-223  729.0   0.3    1.0  1  lcl|FitnessBrowser__BFirm:BPHYT_RS19500  BPHYT_RS19500 methylmalonate-sem


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__BFirm:BPHYT_RS19500  BPHYT_RS19500 methylmalonate-semialdehyde dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  729.0   0.3  1.2e-223  1.2e-223       2     477 .]      20     496 ..      19     496 .. 1.00

  Alignments for each domain:
  == domain 1  score: 729.0 bits;  conditional E-value: 1.2e-223
                                TIGR01722   2 khlidGkfvegksdkyipvsnpatnevlakvaeasaeevdaavasaretfaawaetsvaerarvllryqa 71 
                                               h+i+Gk+ eg+s+++++v npa+++v a+v+ as++evdaava+a+ +f+aw+et+  +rarvl+++++
  lcl|FitnessBrowser__BFirm:BPHYT_RS19500  20 THFINGKTFEGTSGRFGDVFNPAQGSVSARVPLASVAEVDAAVAAAKAAFPAWSETAPIKRARVLFKFKE 89 
                                              69******************************************************************** PP

                                TIGR01722  72 llkehrdeiaklisaeqGktledakGdvarGlevvehacsvtslllGetvesvakdvdvysirqplGvva 141
                                              ll+ h+de+a+li+ e+Gk+++dakG+v+rG+e+ve+ac+++ ll+ + ++++   +d + +rqplGvva
  lcl|FitnessBrowser__BFirm:BPHYT_RS19500  90 LLDRHHDELAELITREHGKVFSDAKGEVMRGIEIVEFACGIPNLLKTDFTDQIGGGIDNWNLRQPLGVVA 159
                                              ********************************************************************** PP

                                TIGR01722 142 GitpfnfpamiplwmfplaiacGntfvlkpsekvpsaavklaellseaGapdGvlnvvhGdkeavdrlle 211
                                              Gitpfnfp m+p wmfp+aiacGntfvlkpse++ps++ +laell+eaG+pdGv+nvvhGdk+avd ll 
  lcl|FitnessBrowser__BFirm:BPHYT_RS19500 160 GITPFNFPMMVPCWMFPVAIACGNTFVLKPSERDPSCSNRLAELLKEAGLPDGVFNVVHGDKVAVDALLV 229
                                              ********************************************************************** PP

                                TIGR01722 212 hpdvkavsfvGsvavgeyiyetgsahgkrvqalaGaknhmvvlpdadkeaaldalvgaavGaaGqrcmai 281
                                              hp+v a+sfvGs++++eyiy+ g++hgkrvqal+Gaknh vv+pdad+++a+dal+gaa+G+aG+rcmai
  lcl|FitnessBrowser__BFirm:BPHYT_RS19500 230 HPEVSALSFVGSTPIAEYIYTEGTKHGKRVQALGGAKNHLVVMPDADLDQAVDALIGAAYGSAGERCMAI 299
                                              ********************************************************************** PP

                                TIGR01722 282 saavlvGaa.kelveeireraekvrvgagddpgaelGplitkqakervasliasgakeGaevlldGrgyk 350
                                              s+av+vG + +el+e++  r++ +++  g ++ ae+Gpl+t  ++e+v  +i+sg++ Ga++++dGrg +
  lcl|FitnessBrowser__BFirm:BPHYT_RS19500 300 SVAVAVGHIaDELIERLTPRVKSLKILNGMESDAEMGPLVTAVHREKVVGYIDSGVEAGAKLVVDGRGHQ 369
                                              *******988************************************************************ PP

                                TIGR01722 351 veGyeeGnfvGitllervkpdmkiykeeifGpvlvvleadtleeaiklinespyGnGtaiftsdGaaark 420
                                              v G+e+G f+G tl+++v +dmkiy+eeifGpvl+v+++  +  a++lin++ + nG ++ftsdG+ ar 
  lcl|FitnessBrowser__BFirm:BPHYT_RS19500 370 VSGHEKGFFLGGTLFDNVSTDMKIYREEIFGPVLCVVRVPDFASAVELINANEFANGVSLFTSDGGVARA 439
                                              ********************************************************************** PP

                                TIGR01722 421 fqheievGqvGvnvpipvplpffsftGwkdslfGdlhiyGkqGvrfytrlktvtarw 477
                                              f+ +i++G+vG+nvpipvp++++sf+Gwk+slfGd+h+yG++Gvrfytr k +  rw
  lcl|FitnessBrowser__BFirm:BPHYT_RS19500 440 FSRQIQIGMVGINVPIPVPMAWHSFGGWKKSLFGDHHAYGEEGVRFYTRYKSIMQRW 496
                                              ********************************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (477 nodes)
Target sequences:                          1  (512 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: 00:00:00.02
# Mc/sec: 11.29
//
[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