Alignments for a candidate for mmsA in Sinorhizobium meliloti 1021

GapMind for catabolism of small carbon sources

Alignments for a candidate for mmsA in Sinorhizobium meliloti 1021

Align Methylmalonate-semialdehyde dehydrogenase [inositol] (EC 1.2.1.27) (characterized)
to candidate SMc00781 SMc00781 malonic semialdehyde oxidative decarboxylase

Query= reanno::Caulo:CCNA_01360
         (500 letters)



>FitnessBrowser__Smeli:SMc00781
          Length = 498

 Score =  644 bits (1662), Expect = 0.0
 Identities = 318/500 (63%), Positives = 384/500 (76%), Gaps = 3/500 (0%)

Query: 2   MRDIPHFIGGQKVDGASGRFGEVFDPNTGKVQARVALASAGELNTAIANAKVAQAAWAAT 61
           M ++ HFI G++V G SGR   +F+P TG+VQ  VALAS  +L  A+ +AK AQ  WAAT
Sbjct: 1   MYELGHFIDGKRVAGTSGRVSNIFNPATGEVQGTVALASDADLAAAVESAKAAQPKWAAT 60

Query: 62  NPQRRARVMFEFKRLLEVHMDELAALLSSEHGKVIADSKGDIQRGLEVIEFACGVPHLLK 121
           NPQRRARV  +F +LL  +M+ELA +LS EHGK I D+KGDI RGLEV EF  G+PHL K
Sbjct: 61  NPQRRARVFMKFVQLLNDNMNELAEMLSREHGKTIDDAKGDIVRGLEVCEFVIGIPHLQK 120

Query: 122 GEYTQGAGPGIDVYSMRQPLGVVAGITPFNFPAMIPMWMFGPAIATGNAFILKPSERDPS 181
            E+T+GAGPGID+YS+RQP+G+ AGITPFNFP MIPMWMF PAIA GNAFILKPSERDPS
Sbjct: 121 SEFTEGAGPGIDMYSIRQPVGIGAGITPFNFPGMIPMWMFAPAIACGNAFILKPSERDPS 180

Query: 182 VPVRLAELMIEAGLPPGVLNVVHGDKDCVEAILDHPDIKAVSFVGSSDIAQSVFQRAGAA 241
           VP+RLAELMIEAGLP G+LNVV+GDK  V+AIL HPDI AVSFVGS+ IA+ V+  A   
Sbjct: 181 VPIRLAELMIEAGLPAGILNVVNGDKGAVDAILTHPDIAAVSFVGSTPIARYVYGTAAMN 240

Query: 242 GKRVQAMGGAKNHGLVMPDADLDQAVADIIGAAYGSAGERCMALPVVVPVGEKTATALRE 301
           GKR Q  GGAKNH ++MPDADLDQA   +IGA YGSAGERCMA+ V VPVGE+TA  L +
Sbjct: 241 GKRAQCFGGAKNHMIIMPDADLDQAANALIGAGYGSAGERCMAISVAVPVGEETANRLID 300

Query: 302 KLVAAIGGLRVGVSTDPDAHYGPVVSAAHKARIESYIQMGVDEGAELVVDGRGFSLQGHE 361
           KLV  +  LR+G  TD  A  GPVV+   + RI S I  G+++GA+LVVDGR F LQG+E
Sbjct: 301 KLVPMVESLRIGPYTDEKADMGPVVTKEAEQRIRSLIDSGIEQGAKLVVDGRDFKLQGYE 360

Query: 362 EGFFVGPTLFDHVKPTSRSYHDEIFGPVLQMVRAESLEEGIALASRHQYGNGVAIFTRNG 421
            G F+G  LFD V P    Y  EIFGPVL +VRA + EE ++L  +H+YGNGVAI+TR+G
Sbjct: 361 NGHFIGGCLFDDVTPDMDIYKTEIFGPVLSVVRARNYEEALSLPMKHEYGNGVAIYTRDG 420

Query: 422 DAAREFADQVEVGMVGINVPIPVPVAYHSFGGWKRSGFGDLNQYGMDGVRFYTRTKTVTQ 481
           DAAR+FA ++ +GMVG+NVPIPVP+AYHSFGGWK S FGDLNQ+G D ++F+TRTKT+T 
Sbjct: 421 DAARDFASRINIGMVGVNVPIPVPLAYHSFGGWKSSSFGDLNQHGTDSIKFWTRTKTITS 480

Query: 482 RWPKGGAVLD-QSFVIPTMR 500
           RWP G  + D   F IPTMR
Sbjct: 481 RWPSG--IKDGAEFSIPTMR 498


Lambda     K      H
   0.320    0.137    0.409 

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: 831
Number of extensions: 30
Number of successful extensions: 1
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: 500
Length of database: 498
Length adjustment: 34
Effective length of query: 466
Effective length of database: 464
Effective search space:   216224
Effective search space used:   216224
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 (21.8 bits)
S2: 52 (24.6 bits)

Align candidate SMc00781 SMc00781 (malonic semialdehyde oxidative decarboxylase)
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.27249.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   7.6e-199  647.2   0.1   8.6e-199  647.0   0.1    1.0  1  lcl|FitnessBrowser__Smeli:SMc00781  SMc00781 malonic semialdehyde ox


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Smeli:SMc00781  SMc00781 malonic semialdehyde oxidative decarboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  647.0   0.1  8.6e-199  8.6e-199       3     477 .]       6     482 ..       4     482 .. 0.99

  Alignments for each domain:
  == domain 1  score: 647.0 bits;  conditional E-value: 8.6e-199
                           TIGR01722   3 hlidGkfvegksdkyipvsnpatnevlakvaeasaeevdaavasaretfaawaetsvaerarvllryqallkehr 77 
                                         h+idGk v g+s++  ++ npat+ev + va as +++ aav sa+ + + wa t+  +rarv++++ +ll+++ 
  lcl|FitnessBrowser__Smeli:SMc00781   6 HFIDGKRVAGTSGRVSNIFNPATGEVQGTVALASDADLAAAVESAKAAQPKWAATNPQRRARVFMKFVQLLNDNM 80 
                                         9************************************************************************** PP

                           TIGR01722  78 deiaklisaeqGktledakGdvarGlevvehacsvtslllGetvesvakdvdvysirqplGvvaGitpfnfpami 152
                                         +e+a+++s e+Gkt++dakGd++rGlev e+  +++ l + e +e     +d+ysirqp+G+ aGitpfnfp mi
  lcl|FitnessBrowser__Smeli:SMc00781  81 NELAEMLSREHGKTIDDAKGDIVRGLEVCEFVIGIPHLQKSEFTEGAGPGIDMYSIRQPVGIGAGITPFNFPGMI 155
                                         *************************************************************************** PP

                           TIGR01722 153 plwmfplaiacGntfvlkpsekvpsaavklaellseaGapdGvlnvvhGdkeavdrllehpdvkavsfvGsvavg 227
                                         p+wmf  aiacGn+f+lkpse++ps  ++lael+ eaG+p G+lnvv Gdk avd +l hpd+ avsfvGs++++
  lcl|FitnessBrowser__Smeli:SMc00781 156 PMWMFAPAIACGNAFILKPSERDPSVPIRLAELMIEAGLPAGILNVVNGDKGAVDAILTHPDIAAVSFVGSTPIA 230
                                         *************************************************************************** PP

                           TIGR01722 228 eyiyetgsahgkrvqalaGaknhmvvlpdadkeaaldalvgaavGaaGqrcmaisaavlvGaa..kelveeirer 300
                                         +y+y t++ +gkr q+++Gaknhm+++pdad+++a++al+ga +G+aG+rcmais+av vG+   ++l+++++  
  lcl|FitnessBrowser__Smeli:SMc00781 231 RYVYGTAAMNGKRAQCFGGAKNHMIIMPDADLDQAANALIGAGYGSAGERCMAISVAVPVGEEtaNRLIDKLVPM 305
                                         *************************************************************854599******** PP

                           TIGR01722 301 aekvrvgagddpgaelGplitkqakervasliasgakeGaevlldGrgykveGyeeGnfvGitllervkpdmkiy 375
                                         +e +r+g+++d  a++Gp++tk+a +r+ sli+sg+++Ga++++dGr +k++Gye+G+f+G +l+++v pdm iy
  lcl|FitnessBrowser__Smeli:SMc00781 306 VESLRIGPYTDEKADMGPVVTKEAEQRIRSLIDSGIEQGAKLVVDGRDFKLQGYENGHFIGGCLFDDVTPDMDIY 380
                                         *************************************************************************** PP

                           TIGR01722 376 keeifGpvlvvleadtleeaiklinespyGnGtaiftsdGaaarkfqheievGqvGvnvpipvplpffsftGwkd 450
                                         k eifGpvl v++a  +eea+ l  +  yGnG ai+t+dG aar f  +i++G+vGvnvpipvpl+++sf+Gwk+
  lcl|FitnessBrowser__Smeli:SMc00781 381 KTEIFGPVLSVVRARNYEEALSLPMKHEYGNGVAIYTRDGDAARDFASRINIGMVGVNVPIPVPLAYHSFGGWKS 455
                                         *************************************************************************** PP

                           TIGR01722 451 slfGdlhiyGkqGvrfytrlktvtarw 477
                                         s fGdl+ +G + ++f+tr+kt+t+rw
  lcl|FitnessBrowser__Smeli:SMc00781 456 SSFGDLNQHGTDSIKFWTRTKTITSRW 482
                                         *************************** PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (477 nodes)
Target sequences:                          1  (498 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: 10.90
//
[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