Alignments for a candidate for mmsA in Halomonas desiderata SP1

GapMind for catabolism of small carbon sources

Alignments for a candidate for mmsA in Halomonas desiderata SP1

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_086510928.1 BZY95_RS16190 methylmalonate-semialdehyde dehydrogenase (CoA acylating)

Query= BRENDA::A0A081YAY7
         (498 letters)



>NCBI__GCF_002151265.1:WP_086510928.1
          Length = 503

 Score =  606 bits (1562), Expect = e-178
 Identities = 302/499 (60%), Positives = 376/499 (75%), Gaps = 7/499 (1%)

Query: 4   IKHLIGGELIA-DTGRTADVFNPSTGEAVRKVPLADRETMQQAIDAAKAAFPAWRNTPPA 62
           I H I G++ + ++GR   V+NP+TG+   +V LA R  +  A+ AAKAAFPAW +TPP 
Sbjct: 6   IAHYIAGQMTSGESGRHQSVYNPATGQVTGQVALASRADVATAVAAAKAAFPAWADTPPI 65

Query: 63  KRAQVLFRFKQLLEANEERIVKLISEEHGKTIEDAAGELKRGIENVEYATAAPEILKGEY 122
           +RA+VLF+F +LL AN++ + + I+ EHGK   DA GE+ RGI+ VE+A   P++LKG++
Sbjct: 66  RRARVLFKFLELLNANKDELARAITLEHGKVFTDAQGEVARGIDIVEFACGIPQLLKGDF 125

Query: 123 SRNVGPNIDAWSDFQPIGVVAGITPFNFPAMVPLWMYPLAIACGNTFILKPSERDPSSTL 182
           +  V   ID W+  QP+GVVAGITPFNFPAMVP+WM+P+AIA GNTFILKPS  DPS++L
Sbjct: 126 TEQVSNGIDNWTVRQPLGVVAGITPFNFPAMVPMWMFPVAIAAGNTFILKPSPTDPSASL 185

Query: 183 LIAELFHEAGLPKGVLNVVHGDKGAVDALIEAPEVKALSFVGSTPIAEYIYSEGTKRGKR 242
           LIAEL  +AGLP GV NVV GDK +VDALIE P+V+ALSFVGSTPIA  IY  G + GKR
Sbjct: 186 LIAELLKQAGLPDGVFNVVQGDKESVDALIEHPDVQALSFVGSTPIANLIYENGARHGKR 245

Query: 243 VQALGGAKNHAVLMPDADLDNAVSALMGAAYGSCGERCMAISVAVCVGDQIADALVQKLV 302
           VQALGGAKNH V+MPDADLD AV AL+GAAYGS GERCMAISVAV VGD +AD +V +L 
Sbjct: 246 VQALGGAKNHMVVMPDADLDKAVDALIGAAYGSAGERCMAISVAVLVGD-VADKIVPRLA 304

Query: 303 PQIKGLKIGAGTSCGLDMGPLVTGAARDKVTGYIDTGVAQGAELVVDGRGYKVA----GH 358
            + + LK+  G     +MGP+VT  A  ++TGYI+ GVA+GAELVVDGR +  A    G 
Sbjct: 305 ERARALKVKNGLELDAEMGPIVTAQAHQRITGYIEKGVAEGAELVVDGREFDAATTGDGC 364

Query: 359 ENGFFLGGTLFDRVTPEMTIYKEEIFGPVLCIVRVNSLEEAMQLINDHEYGNGTCIFTRD 418
             GF++GG+LFD VTPEMTIYKEEIFGPVL  VRV  +  A+QLINDHE+GNG   FT  
Sbjct: 365 GEGFWMGGSLFDHVTPEMTIYKEEIFGPVLACVRVPDVATAIQLINDHEFGNGVSCFTES 424

Query: 419 GEAARLFCDEIEVGMVGVNVPLPVPVAYHSFGGWKRSLFGDLHAYGPDGVRFYTKRKAIT 478
           G  AR F   I+VGMVG+NVP+PVP+A+H FGGWKRSLFGD HAYG +GVRFYTK+K+I 
Sbjct: 425 GSVAREFGRRIQVGMVGINVPIPVPMAWHGFGGWKRSLFGDTHAYGEEGVRFYTKQKSIM 484

Query: 479 QRWPQRKSHEAAQFAFPSN 497
           QRW     +  A+FA P++
Sbjct: 485 QRWSD-SINAGAEFAMPTH 502


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: 767
Number of extensions: 24
Number of successful extensions: 3
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: 503
Length adjustment: 34
Effective length of query: 464
Effective length of database: 469
Effective search space:   217616
Effective search space used:   217616
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_086510928.1 BZY95_RS16190 (methylmalonate-semialdehyde dehydrogenase (CoA acylating))
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.11020.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.2e-210  686.2   1.2   1.3e-210  686.0   1.2    1.0  1  lcl|NCBI__GCF_002151265.1:WP_086510928.1  BZY95_RS16190 methylmalonate-sem


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_002151265.1:WP_086510928.1  BZY95_RS16190 methylmalonate-semialdehyde dehydrogenase (CoA acylating)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  686.0   1.2  1.3e-210  1.3e-210       2     477 .]       7     487 ..       6     487 .. 0.99

  Alignments for each domain:
  == domain 1  score: 686.0 bits;  conditional E-value: 1.3e-210
                                 TIGR01722   2 khlidGkfvegksdkyipvsnpatnevlakvaeasaeevdaavasaretfaawaetsvaerarvllryq 70 
                                                h+i+G++  g+s+++  v npat++v+++va as ++v +ava+a+ +f+awa+t+  +rarvl+++ 
  lcl|NCBI__GCF_002151265.1:WP_086510928.1   7 AHYIAGQMTSGESGRHQSVYNPATGQVTGQVALASRADVATAVAAAKAAFPAWADTPPIRRARVLFKFL 75 
                                               69******************************************************************* PP

                                 TIGR01722  71 allkehrdeiaklisaeqGktledakGdvarGlevvehacsvtslllGetvesvakdvdvysirqplGv 139
                                               +ll++++de+a+ i++e+Gk+++da+G+varG+++ve+ac+++ ll+G+ +e+v++ +d +++rqplGv
  lcl|NCBI__GCF_002151265.1:WP_086510928.1  76 ELLNANKDELARAITLEHGKVFTDAQGEVARGIDIVEFACGIPQLLKGDFTEQVSNGIDNWTVRQPLGV 144
                                               ********************************************************************* PP

                                 TIGR01722 140 vaGitpfnfpamiplwmfplaiacGntfvlkpsekvpsaavklaellseaGapdGvlnvvhGdkeavdr 208
                                               vaGitpfnfpam+p+wmfp+aia Gntf+lkps  +psa++ +aell++aG+pdGv+nvv Gdke+vd 
  lcl|NCBI__GCF_002151265.1:WP_086510928.1 145 VAGITPFNFPAMVPMWMFPVAIAAGNTFILKPSPTDPSASLLIAELLKQAGLPDGVFNVVQGDKESVDA 213
                                               ********************************************************************* PP

                                 TIGR01722 209 llehpdvkavsfvGsvavgeyiyetgsahgkrvqalaGaknhmvvlpdadkeaaldalvgaavGaaGqr 277
                                               l+ehpdv+a+sfvGs+++++ iye+g++hgkrvqal+Gaknhmvv+pdad+++a+dal+gaa+G+aG+r
  lcl|NCBI__GCF_002151265.1:WP_086510928.1 214 LIEHPDVQALSFVGSTPIANLIYENGARHGKRVQALGGAKNHMVVMPDADLDKAVDALIGAAYGSAGER 282
                                               ********************************************************************* PP

                                 TIGR01722 278 cmaisaavlvGaa.kelveeireraekvrvgagddpgaelGplitkqakervasliasgakeGaevlld 345
                                               cmais+avlvG++ +++v+++ era+ ++v  g +  ae+Gp++t qa++r++ +i++g++eGae+++d
  lcl|NCBI__GCF_002151265.1:WP_086510928.1 283 CMAISVAVLVGDVaDKIVPRLAERARALKVKNGLELDAEMGPIVTAQAHQRITGYIEKGVAEGAELVVD 351
                                               ************989****************************************************** PP

                                 TIGR01722 346 Grgy....kveGyeeGnfvGitllervkpdmkiykeeifGpvlvvleadtleeaiklinespyGnGtai 410
                                               Gr +    + +G  eG ++G +l+++v p+m+iykeeifGpvl+ +++  +  ai+lin+  +GnG + 
  lcl|NCBI__GCF_002151265.1:WP_086510928.1 352 GREFdaatTGDGCGEGFWMGGSLFDHVTPEMTIYKEEIFGPVLACVRVPDVATAIQLINDHEFGNGVSC 420
                                               *987222256999******************************************************** PP

                                 TIGR01722 411 ftsdGaaarkfqheievGqvGvnvpipvplpffsftGwkdslfGdlhiyGkqGvrfytrlktvtarw 477
                                               ft++G+ ar+f  +i+vG+vG+nvpipvp++++ f+Gwk slfGd+h+yG++Gvrfyt++k +  rw
  lcl|NCBI__GCF_002151265.1:WP_086510928.1 421 FTESGSVAREFGRRIQVGMVGINVPIPVPMAWHGFGGWKRSLFGDTHAYGEEGVRFYTKQKSIMQRW 487
                                               ******************************************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (477 nodes)
Target sequences:                          1  (503 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: 12.75
//
[ok]

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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Steps (tab-delimited)
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Protein sequences (fasta format)
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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