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.21934.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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.01
# Mc/sec: 12.23
//
[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