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.24913.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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 8.28
//
[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:

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:

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:

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:

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