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.19506.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: 0.01u 0.02s 00:00:00.03 Elapsed: 00:00:00.03
# Mc/sec: 7.04
//
[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