Alignments for a candidate for mmsA in Erythrobacter marinus HWDM-33

GapMind for catabolism of small carbon sources

Alignments for a candidate for mmsA in Erythrobacter marinus HWDM-33

Align Methylmalonate-semialdehyde dehydrogenase [inositol] (EC 1.2.1.27) (characterized)
to candidate WP_047092853.1 AAV99_RS05730 CoA-acylating methylmalonate-semialdehyde dehydrogenase

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



>NCBI__GCF_001013305.1:WP_047092853.1
          Length = 498

 Score =  737 bits (1902), Expect = 0.0
 Identities = 360/498 (72%), Positives = 411/498 (82%), Gaps = 1/498 (0%)

Query: 2   MRDIPHFIGGQKVDGASGRFGEVFDPNTGKVQARVALASAGELNTAIANAKVAQAAWAAT 61
           MR + HFI G    G SGR  ++++P+TG+VQA VAL  A  L+ A+ NAK  Q  WAAT
Sbjct: 1   MRQVDHFIQGGSGSG-SGRTHKIWNPSTGEVQAEVALGDAALLDRAMENAKKVQPEWAAT 59

Query: 62  NPQRRARVMFEFKRLLEVHMDELAALLSSEHGKVIADSKGDIQRGLEVIEFACGVPHLLK 121
           NPQ+RARVMF+FK L+E +M +LA LLSSEHGKV+ D+KGD+QRGLEVIE+ACG+P +LK
Sbjct: 60  NPQKRARVMFKFKELIEANMQDLAELLSSEHGKVVDDAKGDVQRGLEVIEYACGIPQVLK 119

Query: 122 GEYTQGAGPGIDVYSMRQPLGVVAGITPFNFPAMIPMWMFGPAIATGNAFILKPSERDPS 181
           GEYTQGAGPGIDVYS RQPLG+ AGITPFNFPAMIPMWMFG AIA GNAFILKPSERDPS
Sbjct: 120 GEYTQGAGPGIDVYSTRQPLGIGAGITPFNFPAMIPMWMFGMAIAAGNAFILKPSERDPS 179

Query: 182 VPVRLAELMIEAGLPPGVLNVVHGDKDCVEAILDHPDIKAVSFVGSSDIAQSVFQRAGAA 241
           VPVRLAEL +EAG P G+L VVHGDK+ V+AILDHPDI AVSFVGSSDIAQ ++ R  A 
Sbjct: 180 VPVRLAELFLEAGAPEGLLQVVHGDKEMVDAILDHPDIAAVSFVGSSDIAQYIYSRGTAN 239

Query: 242 GKRVQAMGGAKNHGLVMPDADLDQAVADIIGAAYGSAGERCMALPVVVPVGEKTATALRE 301
            KRVQA GGAKNHG+VMPDADLDQ V D+ GAA+GSAGERCMALPVVVPVGE TA  LRE
Sbjct: 240 AKRVQAFGGAKNHGVVMPDADLDQVVNDLAGAAFGSAGERCMALPVVVPVGEDTANRLRE 299

Query: 302 KLVAAIGGLRVGVSTDPDAHYGPVVSAAHKARIESYIQMGVDEGAELVVDGRGFSLQGHE 361
           KL+ AI  LR+GVS DPDAHYGPVV+  HKARIE +I    +EG E+VVDGRG+SLQGHE
Sbjct: 300 KLIPAINALRIGVSNDPDAHYGPVVTPEHKARIEEWITTAENEGGEIVVDGRGYSLQGHE 359

Query: 362 EGFFVGPTLFDHVKPTSRSYHDEIFGPVLQMVRAESLEEGIALASRHQYGNGVAIFTRNG 421
           +GFFVGPTL DHV P   SY +EIFGPVLQ+VRA   E  + L S HQYGNGVAIFTRNG
Sbjct: 360 KGFFVGPTLIDHVTPEMESYKEEIFGPVLQIVRATDFEHALRLPSEHQYGNGVAIFTRNG 419

Query: 422 DAAREFADQVEVGMVGINVPIPVPVAYHSFGGWKRSGFGDLNQYGMDGVRFYTRTKTVTQ 481
            AAREFA +V VGMVGINVPIPVPVAYHSFGGWKRSGFGD++QYG +G++F+T+TK VTQ
Sbjct: 420 HAAREFASRVNVGMVGINVPIPVPVAYHSFGGWKRSGFGDIDQYGTEGLKFWTKTKKVTQ 479

Query: 482 RWPKGGAVLDQSFVIPTM 499
           RWP GG     +F+IPTM
Sbjct: 480 RWPDGGGDGSNAFIIPTM 497


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: 900
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 WP_047092853.1 AAV99_RS05730 (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.1635204.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   7.1e-201  653.9   0.1   8.1e-201  653.7   0.1    1.0  1  NCBI__GCF_001013305.1:WP_047092853.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001013305.1:WP_047092853.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  653.7   0.1  8.1e-201  8.1e-201       1     477 []       4     481 ..       4     481 .. 0.98

  Alignments for each domain:
  == domain 1  score: 653.7 bits;  conditional E-value: 8.1e-201
                             TIGR01722   1 vkhlidGkfvegksdkyipvsnpatnevlakvaeasaeevdaavasaretfaawaetsvaerarvllryqall 73 
                                           v h+i+G    g s++  ++ np t+ev a+va   a+ +d a+  a++  + wa t+  +rarv++++++l+
  NCBI__GCF_001013305.1:WP_047092853.1   4 VDHFIQGGSGSG-SGRTHKIWNPSTGEVQAEVALGDAALLDRAMENAKKVQPEWAATNPQKRARVMFKFKELI 75 
                                           689999987655.677889****************************************************** PP

                             TIGR01722  74 kehrdeiaklisaeqGktledakGdvarGlevvehacsvtslllGetvesvakdvdvysirqplGvvaGitpf 146
                                           +++ +++a+l+s+e+Gk+++dakGdv rGlev+e+ac+++  l+Ge ++     +dvys rqplG+ aGitpf
  NCBI__GCF_001013305.1:WP_047092853.1  76 EANMQDLAELLSSEHGKVVDDAKGDVQRGLEVIEYACGIPQVLKGEYTQGAGPGIDVYSTRQPLGIGAGITPF 148
                                           ************************************************************************* PP

                             TIGR01722 147 nfpamiplwmfplaiacGntfvlkpsekvpsaavklaellseaGapdGvlnvvhGdkeavdrllehpdvkavs 219
                                           nfpamip+wmf +aia Gn+f+lkpse++ps  v+lael++eaGap+G l+vvhGdke vd +l+hpd+ avs
  NCBI__GCF_001013305.1:WP_047092853.1 149 NFPAMIPMWMFGMAIAAGNAFILKPSERDPSVPVRLAELFLEAGAPEGLLQVVHGDKEMVDAILDHPDIAAVS 221
                                           ************************************************************************* PP

                             TIGR01722 220 fvGsvavgeyiyetgsahgkrvqalaGaknhmvvlpdadkeaaldalvgaavGaaGqrcmaisaavlvGaa.. 290
                                           fvGs+++++yiy++g+a++krvqa++Gaknh+vv+pdad+++++++l gaa+G+aG+rcma+ ++v vG+   
  NCBI__GCF_001013305.1:WP_047092853.1 222 FVGSSDIAQYIYSRGTANAKRVQAFGGAKNHGVVMPDADLDQVVNDLAGAAFGSAGERCMALPVVVPVGEDta 294
                                           *********************************************************************8544 PP

                             TIGR01722 291 kelveeireraekvrvgagddpgaelGplitkqakervasliasgakeGaevlldGrgykveGyeeGnfvGit 363
                                           ++l e++  +++ +r+g  +dp a++Gp++t+++k+r++++i+++ +eG e+++dGrgy ++G+e+G fvG+t
  NCBI__GCF_001013305.1:WP_047092853.1 295 NRLREKLIPAINALRIGVSNDPDAHYGPVVTPEHKARIEEWITTAENEGGEIVVDGRGYSLQGHEKGFFVGPT 367
                                           8999********************************************************************* PP

                             TIGR01722 364 llervkpdmkiykeeifGpvlvvleadtleeaiklinespyGnGtaiftsdGaaarkfqheievGqvGvnvpi 436
                                           l+++v p+m+ ykeeifGpvl +++a  +e+a++l  e  yGnG aift++G aar+f  +++vG+vG+nvpi
  NCBI__GCF_001013305.1:WP_047092853.1 368 LIDHVTPEMESYKEEIFGPVLQIVRATDFEHALRLPSEHQYGNGVAIFTRNGHAAREFASRVNVGMVGINVPI 440
                                           ************************************************************************* PP

                             TIGR01722 437 pvplpffsftGwkdslfGdlhiyGkqGvrfytrlktvtarw 477
                                           pvp++++sf+Gwk s fGd + yG +G++f+t++k vt rw
  NCBI__GCF_001013305.1:WP_047092853.1 441 PVPVAYHSFGGWKRSGFGDIDQYGTEGLKFWTKTKKVTQRW 481
                                           ***************************************** 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 21.95
//
[ok]

This GapMind analysis is from Sep 24 2021. 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