Alignments for a candidate for mmsA in Marinobacter adhaerens HP15

GapMind for catabolism of small carbon sources

Alignments for a candidate for mmsA in Marinobacter adhaerens HP15

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 GFF2711 HP15_2655 methylmalonate-semialdehyde dehydrogenase

Query= BRENDA::A0A081YAY7
         (498 letters)



>FitnessBrowser__Marino:GFF2711
          Length = 503

 Score =  601 bits (1549), Expect = e-176
 Identities = 291/498 (58%), Positives = 377/498 (75%), Gaps = 7/498 (1%)

Query: 4   IKHLIGGEL-IADTGRTADVFNPSTGEAVRKVPLADRETMQQAIDAAKAAFPAWRNTPPA 62
           I+H I GE+ +  + ++ DVFNP+TG+   +V LA RE +  A+ AA AAFPAW +TPP 
Sbjct: 6   IQHYINGEISLGTSSQSQDVFNPATGQVTGRVALAGREDVDAAVAAADAAFPAWADTPPI 65

Query: 63  KRAQVLFRFKQLLEANEERIVKLISEEHGKTIEDAAGELKRGIENVEYATAAPEILKGEY 122
           +RA+V+F+F +LL  +++ + + I+ EHGK   DA GE+ RGI+ VE+A   P++LKG+Y
Sbjct: 66  RRARVMFKFLELLNTHKDDLARAITAEHGKVFTDAQGEVARGIDIVEFACGIPQLLKGDY 125

Query: 123 SRNVGPNIDAWSDFQPIGVVAGITPFNFPAMVPLWMYPLAIACGNTFILKPSERDPSSTL 182
           +  V   ID W+  QP+GVVAG+TPFNFPAMVP+WM+P+AIA GNTF+LKPS  DPS++L
Sbjct: 126 TEQVSTGIDNWTTRQPLGVVAGVTPFNFPAMVPMWMFPVAIAAGNTFVLKPSPLDPSASL 185

Query: 183 LIAELFHEAGLPKGVLNVVHGDKGAVDALIEAPEVKALSFVGSTPIAEYIYSEGTKRGKR 242
           +IA+L  +AGLP GV NVV GDK AV+ALIE P+V+ALSFVGSTPIA  +Y +G K GKR
Sbjct: 186 MIADLLKQAGLPDGVFNVVQGDKDAVNALIEHPDVQALSFVGSTPIANLLYEKGAKHGKR 245

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

Query: 303 PQIKGLKIGAGTSCGLDMGPLVTGAARDKVTGYIDTGVAQGAELVVDGRGYKVA----GH 358
            + + LK+  G     +MGP+VT AA  ++TGYID GVA+GAELVVDGRG+  +    G 
Sbjct: 305 ERARSLKVKNGEQLDAEMGPIVTAAAHQRITGYIDKGVAEGAELVVDGRGFDASNTGDGC 364

Query: 359 ENGFFLGGTLFDRVTPEMTIYKEEIFGPVLCIVRVNSLEEAMQLINDHEYGNGTCIFTRD 418
            +GF++GG+LFD VTP+MTIY+EEIFGPVL  VRV  +  A++LINDHE+GNG   FT  
Sbjct: 365 ADGFWMGGSLFDHVTPDMTIYREEIFGPVLACVRVPDIATAIRLINDHEFGNGVSCFTES 424

Query: 419 GEAARLFCDEIEVGMVGVNVPLPVPVAYHSFGGWKRSLFGDLHAYGPDGVRFYTKRKAIT 478
           G  AR F   I+VGMVG+NVP+PVP+A+H FGGWKRS+FGD HAYG +GV+FYT++K+I 
Sbjct: 425 GSVAREFGRRIQVGMVGINVPIPVPMAWHGFGGWKRSMFGDTHAYGEEGVKFYTRQKSIM 484

Query: 479 QRWPQRKSHEAAQFAFPS 496
           QRW        A+F  P+
Sbjct: 485 QRWSD-SIDAGAEFVMPT 501


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: 781
Number of extensions: 25
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 GFF2711 HP15_2655 (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.30481.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   7.6e-210  683.5   0.8   8.6e-210  683.3   0.8    1.0  1  lcl|FitnessBrowser__Marino:GFF2711  HP15_2655 methylmalonate-semiald


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Marino:GFF2711  HP15_2655 methylmalonate-semialdehyde dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  683.3   0.8  8.6e-210  8.6e-210       1     477 []       6     487 ..       6     487 .. 0.99

  Alignments for each domain:
  == domain 1  score: 683.3 bits;  conditional E-value: 8.6e-210
                           TIGR01722   1 vkhlidGkfvegksdkyipvsnpatnevlakvaeasaeevdaavasaretfaawaetsvaerarvllryqallke 75 
                                         ++h+i+G++  g+s++  +v npat++v+++va a  e+vdaava+a  +f+awa+t+  +rarv++++ +ll+ 
  lcl|FitnessBrowser__Marino:GFF2711   6 IQHYINGEISLGTSSQSQDVFNPATGQVTGRVALAGREDVDAAVAAADAAFPAWADTPPIRRARVMFKFLELLNT 80 
                                         58************************************************************************* PP

                           TIGR01722  76 hrdeiaklisaeqGktledakGdvarGlevvehacsvtslllGetvesvakdvdvysirqplGvvaGitpfnfpa 150
                                         h+d++a+ i+ae+Gk+++da+G+varG+++ve+ac+++ ll+G+ +e+v++ +d ++ rqplGvvaG+tpfnfpa
  lcl|FitnessBrowser__Marino:GFF2711  81 HKDDLARAITAEHGKVFTDAQGEVARGIDIVEFACGIPQLLKGDYTEQVSTGIDNWTTRQPLGVVAGVTPFNFPA 155
                                         *************************************************************************** PP

                           TIGR01722 151 miplwmfplaiacGntfvlkpsekvpsaavklaellseaGapdGvlnvvhGdkeavdrllehpdvkavsfvGsva 225
                                         m+p+wmfp+aia Gntfvlkps  +psa++ +a+ll++aG+pdGv+nvv Gdk+av+ l+ehpdv+a+sfvGs++
  lcl|FitnessBrowser__Marino:GFF2711 156 MVPMWMFPVAIAAGNTFVLKPSPLDPSASLMIADLLKQAGLPDGVFNVVQGDKDAVNALIEHPDVQALSFVGSTP 230
                                         *************************************************************************** PP

                           TIGR01722 226 vgeyiyetgsahgkrvqalaGaknhmvvlpdadkeaaldalvgaavGaaGqrcmaisaavlvGaa.kelveeire 299
                                         +++ +ye+g++hgkr+qal+Gaknhmvv+pdad+++a+dal+gaa+G+aG+rcmais+avlvG++ +++v+++ e
  lcl|FitnessBrowser__Marino:GFF2711 231 IANLLYEKGAKHGKRIQALGGAKNHMVVMPDADLDKAVDALIGAAYGSAGERCMAISVAVLVGDVaDKIVPRLAE 305
                                         ****************************************************************989******** PP

                           TIGR01722 300 raekvrvgagddpgaelGplitkqakervasliasgakeGaevlldGrgy....kveGyeeGnfvGitllervkp 370
                                         ra+ ++v  g++  ae+Gp++t +a++r++ +i++g++eGae+++dGrg+    + +G  +G ++G +l+++v p
  lcl|FitnessBrowser__Marino:GFF2711 306 RARSLKVKNGEQLDAEMGPIVTAAAHQRITGYIDKGVAEGAELVVDGRGFdasnTGDGCADGFWMGGSLFDHVTP 380
                                         ************************************************98333345899**************** PP

                           TIGR01722 371 dmkiykeeifGpvlvvleadtleeaiklinespyGnGtaiftsdGaaarkfqheievGqvGvnvpipvplpffsf 445
                                         dm+iy+eeifGpvl+ +++  +  ai+lin+  +GnG + ft++G+ ar+f  +i+vG+vG+nvpipvp++++ f
  lcl|FitnessBrowser__Marino:GFF2711 381 DMTIYREEIFGPVLACVRVPDIATAIRLINDHEFGNGVSCFTESGSVAREFGRRIQVGMVGINVPIPVPMAWHGF 455
                                         *************************************************************************** PP

                           TIGR01722 446 tGwkdslfGdlhiyGkqGvrfytrlktvtarw 477
                                         +Gwk s+fGd+h+yG++Gv+fytr+k +  rw
  lcl|FitnessBrowser__Marino:GFF2711 456 GGWKRSMFGDTHAYGEEGVKFYTRQKSIMQRW 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.03
# Mc/sec: 7.29
//
[ok]

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

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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