Alignments for a candidate for mmsA in Lentibacillus jeotgali Grbi

GapMind for catabolism of small carbon sources

Alignments for a candidate for mmsA in Lentibacillus jeotgali Grbi

Align methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate WP_010531948.1 ON01_RS15275 CoA-acylating methylmalonate-semialdehyde dehydrogenase

Query= BRENDA::P42412
         (487 letters)



>NCBI__GCF_000224785.1:WP_010531948.1
          Length = 488

 Score =  707 bits (1824), Expect = 0.0
 Identities = 337/478 (70%), Positives = 411/478 (85%), Gaps = 2/478 (0%)

Query: 6   KLKNYINGEWVESKTDQYEDVVNPATKEVLCQVPISTKEDIDYAAQTAAEAFKTWSKVAV 65
           +LKNYI G+W+E+K+D+ E V+NPAT EV+ +VPIS+ ED+D+A + A EAF+ W ++AV
Sbjct: 10  QLKNYIGGKWIEAKSDKTESVINPATGEVIAEVPISSNEDVDHAVEVAHEAFQDWKELAV 69

Query: 66  PRRARILFNFQQLLSQHKEELAHLITIENGKNTKEALGEVGRGIENVEFAAGAPSLMMGD 125
           P+RARILF +QQLL  H +ELA LITIENGKN KEA GEV RGIENVEFAAGAP+LMMGD
Sbjct: 70  PKRARILFKYQQLLVDHWDELAELITIENGKNLKEAKGEVQRGIENVEFAAGAPNLMMGD 129

Query: 126 SLASIATDVEAANYRYPIGVVGGIAPFNFPMMVPCWMFPMAIALGNTFILKPSERTPLLT 185
            L+SIA+ +E+  YRYPIGVVGGI PFNFPMMVPCWMFPMAIA GNTFI+KPSERTPLL 
Sbjct: 130 QLSSIASGLESGVYRYPIGVVGGITPFNFPMMVPCWMFPMAIATGNTFIMKPSERTPLLA 189

Query: 186 EKLVELFEKAGLPKGVFNVVYGAHDVVNGILEHPEIKAISFVGSKPVGEYVYKKGSENLK 245
            +L EL E+AGLP+GVFN+V+GAHDVVNG+L+H ++ AISFVGS+PV E+VYK+G++NLK
Sbjct: 190 NRLAELLEEAGLPEGVFNIVHGAHDVVNGLLDHDKVAAISFVGSQPVAEHVYKRGTDNLK 249

Query: 246 RVQSLTGAKNHTIVLNDANLEDTVTNIVGAAFGSAGERCMACAVVTVEEGIADEFMAKLQ 305
           RVQ+L+GAKNHTIVLNDAN+++  T I+ AAFGSAGERCMA +VV VEE +ADEF+ +L 
Sbjct: 250 RVQALSGAKNHTIVLNDANMDNASTQILNAAFGSAGERCMAASVVAVEESVADEFIDQLI 309

Query: 306 EKVADIKIGNGLDDGVFLGPVIREDNKKRTLSYIEKGLEEGARLVCDGRE--NVSDDGYF 363
           +K  +I IGNGLD+ VFLGPVIRE +K+RTL YIE G  EGA+L+ DGRE  N  + GYF
Sbjct: 310 KKANEINIGNGLDEDVFLGPVIREQHKERTLGYIETGENEGAKLIRDGREDGNAQEKGYF 369

Query: 364 VGPTIFDNVTTEMTIWKDEIFAPVLSVIRVKNLKEAIEIANKSEFANGACLFTSNSNAIR 423
           VGPTIFDNVTTEM IW++EIFAPVLS++RVK+L EAI++ N+S FANG+CLFT +  ++R
Sbjct: 370 VGPTIFDNVTTEMKIWQEEIFAPVLSIVRVKDLDEAIDVTNQSPFANGSCLFTRDGGSVR 429

Query: 424 YFRENIDAGMLGINLGVPAPMAFFPFSGWKSSFFGTLHANGKDSVDFYTRKKVVTARY 481
            FRENIDAGMLGIN+GVPAPMAFFPFSGWK SF+G LHANGKDSV+FYTRKKV+T R+
Sbjct: 430 QFRENIDAGMLGINIGVPAPMAFFPFSGWKDSFYGDLHANGKDSVEFYTRKKVMTTRW 487


Lambda     K      H
   0.318    0.136    0.396 

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: 741
Number of extensions: 33
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: 487
Length of database: 488
Length adjustment: 34
Effective length of query: 453
Effective length of database: 454
Effective search space:   205662
Effective search space used:   205662
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 52 (24.6 bits)

Align candidate WP_010531948.1 ON01_RS15275 (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.86967.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.5e-187  609.9   0.1   1.7e-187  609.7   0.1    1.0  1  NCBI__GCF_000224785.1:WP_010531948.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000224785.1:WP_010531948.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  609.7   0.1  1.7e-187  1.7e-187       2     477 .]      12     487 ..      11     487 .. 0.98

  Alignments for each domain:
  == domain 1  score: 609.7 bits;  conditional E-value: 1.7e-187
                             TIGR01722   2 khlidGkfvegksdkyipvsnpatnevlakvaeasaeevdaavasaretfaawaetsvaerarvllryqallk 74 
                                           k +i+Gk +e+ksdk   v npat+ev+a+v+++s+e+vd av  a+e+f+ w+e +v +rar+l++yq+ll 
  NCBI__GCF_000224785.1:WP_010531948.1  12 KNYIGGKWIEAKSDKTESVINPATGEVIAEVPISSNEDVDHAVEVAHEAFQDWKELAVPKRARILFKYQQLLV 84 
                                           789********************************************************************** PP

                             TIGR01722  75 ehrdeiaklisaeqGktledakGdvarGlevvehacsvtslllGetvesvakdvdvysirqplGvvaGitpfn 147
                                           +h de+a+li+ e+Gk l++akG+v rG+e ve+a + + l++G+  +s+a  ++   +r p+Gvv Gitpfn
  NCBI__GCF_000224785.1:WP_010531948.1  85 DHWDELAELITIENGKNLKEAKGEVQRGIENVEFAAGAPNLMMGDQLSSIASGLESGVYRYPIGVVGGITPFN 157
                                           ************************************************************************* PP

                             TIGR01722 148 fpamiplwmfplaiacGntfvlkpsekvpsaavklaellseaGapdGvlnvvhGdkeavdrllehpdvkavsf 220
                                           fp m+p wmfp+aia Gntf++kpse+ p+ a +laell+eaG+p+Gv+n+vhG ++ v+ ll+h +v a+sf
  NCBI__GCF_000224785.1:WP_010531948.1 158 FPMMVPCWMFPMAIATGNTFIMKPSERTPLLANRLAELLEEAGLPEGVFNIVHGAHDVVNGLLDHDKVAAISF 230
                                           ************************************************************************* PP

                             TIGR01722 221 vGsvavgeyiyetgsahgkrvqalaGaknhmvvlpdadkeaaldalvgaavGaaGqrcmaisaavlvGaa.ke 292
                                           vGs++v+e++y++g+ + krvqal+Gaknh++vl da+ ++a  ++++aa+G+aG+rcma s++ +  ++ +e
  NCBI__GCF_000224785.1:WP_010531948.1 231 VGSQPVAEHVYKRGTDNLKRVQALSGAKNHTIVLNDANMDNASTQILNAAFGSAGERCMAASVVAVEESVaDE 303
                                           *************************************************************9865554445** PP

                             TIGR01722 293 lveeireraekvrvgagddpgaelGplitkqakervasliasgakeGaevlldGrgykveGyeeGnfvGitll 365
                                           +++++ ++a+ +++g g d    lGp+i +q+ker   +i++g +eGa+++ dGr    +  e+G fvG+t++
  NCBI__GCF_000224785.1:WP_010531948.1 304 FIDQLIKKANEINIGNGLDEDVFLGPVIREQHKERTLGYIETGENEGAKLIRDGRE-DGNAQEKGYFVGPTIF 375
                                           *******************************************************8.56889*********** PP

                             TIGR01722 366 ervkpdmkiykeeifGpvlvvleadtleeaiklinespyGnGtaiftsdGaaarkfqheievGqvGvnvpipv 438
                                           ++v ++mki++eeif pvl ++++  l+eai + n+sp+ nG+++ft+dG++ r+f+ +i++G++G+n+ +p 
  NCBI__GCF_000224785.1:WP_010531948.1 376 DNVTTEMKIWQEEIFAPVLSIVRVKDLDEAIDVTNQSPFANGSCLFTRDGGSVRQFRENIDAGMLGINIGVPA 448
                                           ************************************************************************* PP

                             TIGR01722 439 plpffsftGwkdslfGdlhiyGkqGvrfytrlktvtarw 477
                                           p++ff f+Gwkds++Gdlh+ Gk+ v+fytr k++t+rw
  NCBI__GCF_000224785.1:WP_010531948.1 449 PMAFFPFSGWKDSFYGDLHANGKDSVEFYTRKKVMTTRW 487
                                           *************************************** PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (477 nodes)
Target sequences:                          1  (488 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: 19.82
//
[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