Alignments for a candidate for mmsA in Actinomyces timonensis 7400942

GapMind for catabolism of small carbon sources

Alignments for a candidate for mmsA in Actinomyces timonensis 7400942

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 WP_026048602.1 A1QA_RS0101845 CoA-acylating methylmalonate-semialdehyde dehydrogenase

Query= BRENDA::A0A081YAY7
         (498 letters)



>NCBI__GCF_000295095.1:WP_026048602.1
          Length = 497

 Score =  484 bits (1245), Expect = e-141
 Identities = 238/491 (48%), Positives = 332/491 (67%), Gaps = 4/491 (0%)

Query: 1   MTLIKHLIGGELIADT--GRTADVFNPSTGEAVRKVPLADRETMQQAIDAAKAAFPAWRN 58
           M  IKH I G     T  GR   + NP TGE  +++  A    +  A++ A+ A  +W  
Sbjct: 1   MKTIKHWINGASYEGTPIGRFP-IENPGTGEVEKELLQASDADLDHAVEVAREAQKSWAG 59

Query: 59  TPPAKRAQVLFRFKQLLEANEERIVKLISEEHGKTIEDAAGELKRGIENVEYATAAPEIL 118
              AKR  ++F+ ++L+ A+ + + +LI EEHGK   DA GE++RG E ++++TA    L
Sbjct: 60  YSLAKRTAIMFKMRELVLAHSDEMARLIVEEHGKNYSDAIGEIQRGRETLDFSTAINLAL 119

Query: 119 KGEYSRNVGPNIDAWSDFQPIGVVAGITPFNFPAMVPLWMYPLAIACGNTFILKPSERDP 178
           KGEYS ++   +D  +  QP+GVVAGI PFNFPAMVP+WM+P+AIA GN FILKP+   P
Sbjct: 120 KGEYSFDISTGVDIHTIRQPLGVVAGICPFNFPAMVPMWMHPVAIATGNAFILKPASATP 179

Query: 179 SSTLLIAELFHEAGLPKGVLNVVHGDKGAVDALIEAPEVKALSFVGSTPIAEYIYSEGTK 238
           S+ LL AEL+ EAGLP GV NVV G++  V  ++E P + A+SFVGSTP+A  I + G  
Sbjct: 180 SAALLTAELYKEAGLPDGVFNVVSGNRTMVTKILEHPGIDAISFVGSTPVAHIIQNTGVS 239

Query: 239 RGKRVQALGGAKNHAVLMPDADLDNAVSALMGAAYGSCGERCMAISVAVCVGDQIADALV 298
            GKRVQALGGA NHA++MPD+DLD A   +  AA+G+ GERCMA+ V V VG    D L 
Sbjct: 240 NGKRVQALGGANNHAIVMPDSDLDFAAQHISAAAFGAAGERCMALPVVVAVGGCGPD-LA 298

Query: 299 QKLVPQIKGLKIGAGTSCGLDMGPLVTGAARDKVTGYIDTGVAQGAELVVDGRGYKVAGH 358
           Q++    + +K+G G   G++MGP++   +++ + G I+ G ++G E+V+DGR   + GH
Sbjct: 299 QRVKAHAEKIKVGYGMDEGVEMGPVIDAKSKEFIIGLINEGESKGGEVVLDGRDLVIPGH 358

Query: 359 ENGFFLGGTLFDRVTPEMTIYKEEIFGPVLCIVRVNSLEEAMQLINDHEYGNGTCIFTRD 418
           ENG FLG T+ D V  +  +Y+EE+FGPVL IV  ++ +EA++++N   +GNG+ IFT D
Sbjct: 359 ENGHFLGPTIVDNVPQDSDLYREEVFGPVLSIVHADTYDEAIKIVNSSPFGNGSAIFTND 418

Query: 419 GEAARLFCDEIEVGMVGVNVPLPVPVAYHSFGGWKRSLFGDLHAYGPDGVRFYTKRKAIT 478
           G  AR F  ++E GMVGVNVP+P PVAY+SFGGWK SL GD H +GP+GV+FYT+ KAIT
Sbjct: 419 GGVARRFQLDVEAGMVGVNVPIPTPVAYYSFGGWKESLLGDTHIHGPEGVKFYTRAKAIT 478

Query: 479 QRWPQRKSHEA 489
            RWP  K++ A
Sbjct: 479 SRWPSEKTYAA 489


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: 684
Number of extensions: 27
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: 497
Length adjustment: 34
Effective length of query: 464
Effective length of database: 463
Effective search space:   214832
Effective search space used:   214832
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 WP_026048602.1 A1QA_RS0101845 (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.3691276.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   8.6e-194  630.5   0.6   9.7e-194  630.4   0.6    1.0  1  NCBI__GCF_000295095.1:WP_026048602.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000295095.1:WP_026048602.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  630.4   0.6  9.7e-194  9.7e-194       1     477 []       4     481 ..       4     481 .. 1.00

  Alignments for each domain:
  == domain 1  score: 630.4 bits;  conditional E-value: 9.7e-194
                             TIGR01722   1 vkhlidGkfvegksdkyipvsnpatnevlakvaeasaeevdaavasaretfaawaetsvaerarvllryqall 73 
                                           +kh+i+G+  eg+   + p++np t+ev  ++ +as +++d av  are+  +wa  s+a+r+ ++++ ++l+
  NCBI__GCF_000295095.1:WP_026048602.1   4 IKHWINGASYEGTPIGRFPIENPGTGEVEKELLQASDADLDHAVEVAREAQKSWAGYSLAKRTAIMFKMRELV 76 
                                           69*********************************************************************** PP

                             TIGR01722  74 kehrdeiaklisaeqGktledakGdvarGlevvehacsvtslllGetvesvakdvdvysirqplGvvaGitpf 146
                                            +h de+a+li+ e+Gk ++da G++ rG e ++++ +++  l+Ge + ++++ vd+++irqplGvvaGi+pf
  NCBI__GCF_000295095.1:WP_026048602.1  77 LAHSDEMARLIVEEHGKNYSDAIGEIQRGRETLDFSTAINLALKGEYSFDISTGVDIHTIRQPLGVVAGICPF 149
                                           ************************************************************************* PP

                             TIGR01722 147 nfpamiplwmfplaiacGntfvlkpsekvpsaavklaellseaGapdGvlnvvhGdkeavdrllehpdvkavs 219
                                           nfpam+p+wm p+aia Gn+f+lkp+   psaa+  ael++eaG+pdGv+nvv G++  v ++lehp + a+s
  NCBI__GCF_000295095.1:WP_026048602.1 150 NFPAMVPMWMHPVAIATGNAFILKPASATPSAALLTAELYKEAGLPDGVFNVVSGNRTMVTKILEHPGIDAIS 222
                                           ************************************************************************* PP

                             TIGR01722 220 fvGsvavgeyiyetgsahgkrvqalaGaknhmvvlpdadkeaaldalvgaavGaaGqrcmaisaavlvGaa.k 291
                                           fvGs++v++ i +tg ++gkrvqal+Ga nh++v+pd+d++ a++++ +aa+GaaG+rcma+ ++v+vG +  
  NCBI__GCF_000295095.1:WP_026048602.1 223 FVGSTPVAHIIQNTGVSNGKRVQALGGANNHAIVMPDSDLDFAAQHISAAAFGAAGERCMALPVVVAVGGCgP 295
                                           *********************************************************************9989 PP

                             TIGR01722 292 elveeireraekvrvgagddpgaelGplitkqakervasliasgakeGaevlldGrgykveGyeeGnfvGitl 364
                                           +l ++++ +aek++vg g d g e+Gp+i  ++ke +  li++g  +G ev+ldGr + + G+e+G+f+G+t+
  NCBI__GCF_000295095.1:WP_026048602.1 296 DLAQRVKAHAEKIKVGYGMDEGVEMGPVIDAKSKEFIIGLINEGESKGGEVVLDGRDLVIPGHENGHFLGPTI 368
                                           9************************************************************************ PP

                             TIGR01722 365 lervkpdmkiykeeifGpvlvvleadtleeaiklinespyGnGtaiftsdGaaarkfqheievGqvGvnvpip 437
                                           +++v+ d   y+ee+fGpvl +++adt++eaik++n sp+GnG+aift+dG+ ar+fq+++e+G+vGvnvpip
  NCBI__GCF_000295095.1:WP_026048602.1 369 VDNVPQDSDLYREEVFGPVLSIVHADTYDEAIKIVNSSPFGNGSAIFTNDGGVARRFQLDVEAGMVGVNVPIP 441
                                           ************************************************************************* PP

                             TIGR01722 438 vplpffsftGwkdslfGdlhiyGkqGvrfytrlktvtarw 477
                                            p++++sf+Gwk+sl Gd+hi+G +Gv+fytr+k++t+rw
  NCBI__GCF_000295095.1:WP_026048602.1 442 TPVAYYSFGGWKESLLGDTHIHGPEGVKFYTRAKAITSRW 481
                                           **************************************** PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (477 nodes)
Target sequences:                          1  (497 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 17.10
//
[ok]

This GapMind analysis is from Sep 24 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 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