Alignments for a candidate for mmsA in Methylobacterium nodulans ORS 2060

GapMind for catabolism of small carbon sources

Alignments for a candidate for mmsA in Methylobacterium nodulans ORS 2060

Align Methylmalonate-semialdehyde dehydrogenase [inositol] (EC 1.2.1.27) (characterized)
to candidate WP_043750830.1 MNOD_RS10495 CoA-acylating methylmalonate-semialdehyde dehydrogenase

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



>NCBI__GCF_000022085.1:WP_043750830.1
          Length = 498

 Score =  683 bits (1763), Expect = 0.0
 Identities = 332/485 (68%), Positives = 393/485 (81%)

Query: 2   MRDIPHFIGGQKVDGASGRFGEVFDPNTGKVQARVALASAGELNTAIANAKVAQAAWAAT 61
           MR++ HFIGG++V G SGR  ++F P TG+V  R+ALAS  E+  AI NA  AQ AWAAT
Sbjct: 1   MREVGHFIGGEQVAGRSGRHSDIFQPMTGEVVGRLALASTAEVRGAIENAARAQPAWAAT 60

Query: 62  NPQRRARVMFEFKRLLEVHMDELAALLSSEHGKVIADSKGDIQRGLEVIEFACGVPHLLK 121
           NPQRRARVM  F  L+   +D LA LL+ EHGK I D+KGDIQRG+EV+EFACG+PHLLK
Sbjct: 61  NPQRRARVMMRFLDLVAREIDSLADLLAREHGKTIPDAKGDIQRGVEVVEFACGIPHLLK 120

Query: 122 GEYTQGAGPGIDVYSMRQPLGVVAGITPFNFPAMIPMWMFGPAIATGNAFILKPSERDPS 181
           GE+T+GAGPGID+YSMRQPLGVVAGITPFNFPAMIPMW F PAIA GNAFILKPSERDP 
Sbjct: 121 GEFTEGAGPGIDIYSMRQPLGVVAGITPFNFPAMIPMWKFAPAIACGNAFILKPSERDPG 180

Query: 182 VPVRLAELMIEAGLPPGVLNVVHGDKDCVEAILDHPDIKAVSFVGSSDIAQSVFQRAGAA 241
           VP+RLAELMIEAGLP G+LNVV+GDK+ V+A+LD   I+AV FVGSSDIAQ V+ RA A+
Sbjct: 181 VPMRLAELMIEAGLPAGILNVVNGDKEAVDALLDDDLIQAVGFVGSSDIAQYVYARATAS 240

Query: 242 GKRVQAMGGAKNHGLVMPDADLDQAVADIIGAAYGSAGERCMALPVVVPVGEKTATALRE 301
           GKR Q  GGAKNH ++MPDAD+DQAV  ++GA YGSAGERCMA+ V VPVGE TA AL  
Sbjct: 241 GKRAQCFGGAKNHMIIMPDADMDQAVDALMGAGYGSAGERCMAVSVAVPVGENTADALMS 300

Query: 302 KLVAAIGGLRVGVSTDPDAHYGPVVSAAHKARIESYIQMGVDEGAELVVDGRGFSLQGHE 361
           KLV  +  L++G STDP A YGP+V+ A   R+ +Y+ +GV EGA+LVVDGRGF +QG+E
Sbjct: 301 KLVPRVESLKIGPSTDPSADYGPLVTRAALERVRNYVDIGVREGAKLVVDGRGFKMQGYE 360

Query: 362 EGFFVGPTLFDHVKPTSRSYHDEIFGPVLQMVRAESLEEGIALASRHQYGNGVAIFTRNG 421
            GF++G  LFDHV P  R Y +EIFGPVL +VRA+   E + L S H+YGNGVAIFTR+G
Sbjct: 361 NGFYLGGCLFDHVAPEMRIYKEEIFGPVLSVVRAKDYAEALRLPSAHEYGNGVAIFTRDG 420

Query: 422 DAAREFADQVEVGMVGINVPIPVPVAYHSFGGWKRSGFGDLNQYGMDGVRFYTRTKTVTQ 481
           DAAR+FA +V VGMVGINVPIPVP+AY++FGGWKRSGFGDLNQ+G D VRFYT+TKTVT 
Sbjct: 421 DAARDFAAKVNVGMVGINVPIPVPLAYYTFGGWKRSGFGDLNQHGPDSVRFYTKTKTVTA 480

Query: 482 RWPKG 486
           RWP G
Sbjct: 481 RWPSG 485


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: 862
Number of extensions: 24
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 WP_043750830.1 MNOD_RS10495 (CoA-acylating 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.2011200.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.5e-199  648.8   0.1   2.8e-199  648.6   0.1    1.0  1  NCBI__GCF_000022085.1:WP_043750830.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000022085.1:WP_043750830.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  648.6   0.1  2.8e-199  2.8e-199       1     477 []       4     482 ..       4     482 .. 0.99

  Alignments for each domain:
  == domain 1  score: 648.6 bits;  conditional E-value: 2.8e-199
                             TIGR01722   1 vkhlidGkfvegksdkyipvsnpatnevlakvaeasaeevdaavasaretfaawaetsvaerarvllryqall 73 
                                           v h+i+G+ v g+s+++ ++ +p+t+ev++++a as++ev  a+  a ++ +awa t+  +rarv++r+  l+
  NCBI__GCF_000022085.1:WP_043750830.1   4 VGHFIGGEQVAGRSGRHSDIFQPMTGEVVGRLALASTAEVRGAIENAARAQPAWAATNPQRRARVMMRFLDLV 76 
                                           679********************************************************************** PP

                             TIGR01722  74 kehrdeiaklisaeqGktledakGdvarGlevvehacsvtslllGetvesvakdvdvysirqplGvvaGitpf 146
                                             + d +a l++ e+Gkt+ dakGd+ rG+evve+ac+++ ll+Ge +e     +d+ys+rqplGvvaGitpf
  NCBI__GCF_000022085.1:WP_043750830.1  77 AREIDSLADLLAREHGKTIPDAKGDIQRGVEVVEFACGIPHLLKGEFTEGAGPGIDIYSMRQPLGVVAGITPF 149
                                           ************************************************************************* PP

                             TIGR01722 147 nfpamiplwmfplaiacGntfvlkpsekvpsaavklaellseaGapdGvlnvvhGdkeavdrllehpdvkavs 219
                                           nfpamip+w f  aiacGn+f+lkpse++p+  ++lael+ eaG+p G+lnvv Gdkeavd ll+   ++av 
  NCBI__GCF_000022085.1:WP_043750830.1 150 NFPAMIPMWKFAPAIACGNAFILKPSERDPGVPMRLAELMIEAGLPAGILNVVNGDKEAVDALLDDDLIQAVG 222
                                           ************************************************************************* PP

                             TIGR01722 220 fvGsvavgeyiyetgsahgkrvqalaGaknhmvvlpdadkeaaldalvgaavGaaGqrcmaisaavlvGaa.. 290
                                           fvGs+++++y+y +++a gkr q+++Gaknhm+++pdad ++a+dal+ga +G+aG+rcma+s+av vG+   
  NCBI__GCF_000022085.1:WP_043750830.1 223 FVGSSDIAQYVYARATASGKRAQCFGGAKNHMIIMPDADMDQAVDALMGAGYGSAGERCMAVSVAVPVGENta 295
                                           *********************************************************************8655 PP

                             TIGR01722 291 kelveeireraekvrvgagddpgaelGplitkqakervasliasgakeGaevlldGrgykveGyeeGnfvGit 363
                                           + l+ +++ r+e +++g+ +dp+a++Gpl+t++a erv ++++ g++eGa++++dGrg+k++Gye+G ++G +
  NCBI__GCF_000022085.1:WP_043750830.1 296 DALMSKLVPRVESLKIGPSTDPSADYGPLVTRAALERVRNYVDIGVREGAKLVVDGRGFKMQGYENGFYLGGC 368
                                           99*********************************************************************** PP

                             TIGR01722 364 llervkpdmkiykeeifGpvlvvleadtleeaiklinespyGnGtaiftsdGaaarkfqheievGqvGvnvpi 436
                                           l+++v p+m+iykeeifGpvl v++a  + ea++l  +  yGnG aift+dG aar f  +++vG+vG+nvpi
  NCBI__GCF_000022085.1:WP_043750830.1 369 LFDHVAPEMRIYKEEIFGPVLSVVRAKDYAEALRLPSAHEYGNGVAIFTRDGDAARDFAAKVNVGMVGINVPI 441
                                           ************************************************************************* PP

                             TIGR01722 437 pvplpffsftGwkdslfGdlhiyGkqGvrfytrlktvtarw 477
                                           pvpl++++f+Gwk s fGdl+ +G + vrfyt++ktvtarw
  NCBI__GCF_000022085.1:WP_043750830.1 442 PVPLAYYTFGGWKRSGFGDLNQHGPDSVRFYTKTKTVTARW 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: 00:00:00.01
# Mc/sec: 20.30
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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 2024 update 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