Alignments for a candidate for mmsA in Shewanella oneidensis MR-1

GapMind for catabolism of small carbon sources

Alignments for a candidate for mmsA in Shewanella oneidensis MR-1

Align Methylmalonate-semialdehyde dehydrogenase [acylating]; MMSDH; EC 1.2.1.27 (characterized)
to candidate 200843 SO1678 methylmalonate-semialdehyde dehydrogenase (NCBI ptt file)

Query= SwissProt::P28810
         (497 letters)



>FitnessBrowser__MR1:200843
          Length = 499

 Score =  751 bits (1938), Expect = 0.0
 Identities = 367/499 (73%), Positives = 415/499 (83%), Gaps = 2/499 (0%)

Query: 1   MSVPVRHLIAGAFVEGLGAQRIPVSNPLDNSTLAEIACASAEQVEQAVASARETFASWKE 60
           M+  V+H I G F  G G  +I V+NP +N+T+A I  A+A++V  A+ASA+  F +WKE
Sbjct: 1   MTTQVKHYIDGEFTAGTGTSQIVVTNPANNATIAVINSATADEVHAAIASAKAAFKTWKE 60

Query: 61  TPVSERARVMLRYQALLKEHHDELAKIVSSELGKTFEDAKGDVWRGIEVVEHACNVPSLL 120
            PVSERARVMLRYQ LLKEHHDELA I++ E GKTFEDAKGDVWRGIEV EHACN+ SLL
Sbjct: 61  VPVSERARVMLRYQHLLKEHHDELATILAHETGKTFEDAKGDVWRGIEVAEHACNIASLL 120

Query: 121 MGETVENVARNIDTYSITQPLGVCVGITPFNFPAMIPLWMFPLAIACGNAFILKPSEQVP 180
           MGETVENVAR+IDTYS TQPLGVC GITPFNFPAMIPLWMFPLAIACGN FILKPSEQ P
Sbjct: 121 MGETVENVARSIDTYSYTQPLGVCAGITPFNFPAMIPLWMFPLAIACGNTFILKPSEQDP 180

Query: 181 LTSVRLAELFLEAGAPKGVLQVVHGGKEQVDQLLKHPQVKAVSFVGSVAVGQYVYHTGTA 240
           +T  RL ELF+EAGAPKGVLQ++HG K  VD LL  P VKA+SFVGSVAVGQY+Y TGT 
Sbjct: 181 MTPQRLVELFVEAGAPKGVLQLIHGDKTAVDILLADPAVKAISFVGSVAVGQYIYKTGTD 240

Query: 241 HNKRVQSFAGAKNHMVIMPDADKAQVISNLVGASVGAAGQRCMAISVAVLVGAAREWIPE 300
           + KRVQ+FAGAKNH VIMPDA+K QVI+NLVGASVGAAGQRCMAISVAV VGAA+EWIPE
Sbjct: 241 NLKRVQAFAGAKNHCVIMPDANKQQVINNLVGASVGAAGQRCMAISVAVFVGAAKEWIPE 300

Query: 301 IRDALAKVRPGPWDDSGASYGPVINPQAKARIERLIGQGVEEGAQLLLDGRGYKVEGYPD 360
           +++ALAKVRPG WDD  A YGP+I+P AK R+ +LI QG EEGAQ LLDG  + V G+  
Sbjct: 301 LKEALAKVRPGLWDDKDAGYGPLISPAAKVRVLKLIAQGKEEGAQCLLDGSDFTVAGFES 360

Query: 361 GNWVGPTLFAGVRPDMAIYREEVFGPVLCLAEVDSLEQAIRLINESPYGNGTSIFTSSGA 420
           GNWVGPT+F  V  DM+IY+EE+FGPVLC  E DSLE AI L+N SPYGNGTSIFT+SGA
Sbjct: 361 GNWVGPTMFTKVTTDMSIYKEEIFGPVLCCMESDSLEDAIELVNASPYGNGTSIFTASGA 420

Query: 421 AARTFQHHIEVGQVGINIPIPVPLPFFSFTGWKGSFYGDLHAYGKQGVRFYTETKTVTAR 480
           AAR +QH IEVGQVGIN+PIPVPLPFFSFTGWKGSFYGD HAYGKQ VRFYTETKT+TAR
Sbjct: 421 AARKYQHEIEVGQVGINVPIPVPLPFFSFTGWKGSFYGDQHAYGKQAVRFYTETKTITAR 480

Query: 481 WFDSD--SVAGTNFSIQMR 497
           WF+SD    AG N SI +R
Sbjct: 481 WFESDIAVAAGPNMSINLR 499


Lambda     K      H
   0.319    0.135    0.406 

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: 830
Number of extensions: 34
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: 497
Length of database: 499
Length adjustment: 34
Effective length of query: 463
Effective length of database: 465
Effective search space:   215295
Effective search space used:   215295
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 200843 SO1678 (methylmalonate-semialdehyde dehydrogenase (NCBI ptt file))
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.4217.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   2.1e-250  817.2   1.6   2.4e-250  817.0   1.6    1.0  1  lcl|FitnessBrowser__MR1:200843  SO1678 methylmalonate-semialdehy


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__MR1:200843  SO1678 methylmalonate-semialdehyde dehydrogenase (NCBI ptt file)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  817.0   1.6  2.4e-250  2.4e-250       1     477 []       5     481 ..       5     481 .. 1.00

  Alignments for each domain:
  == domain 1  score: 817.0 bits;  conditional E-value: 2.4e-250
                       TIGR01722   1 vkhlidGkfvegksdkyipvsnpatnevlakvaeasaeevdaavasaretfaawaetsvaerarvllryqallkehrde 79 
                                     vkh+idG+f  g+++  i v+npa+n ++a +  a+a+ev+aa+asa+ +f +w+e +v+erarv+lryq llkeh+de
  lcl|FitnessBrowser__MR1:200843   5 VKHYIDGEFTAGTGTSQIVVTNPANNATIAVINSATADEVHAAIASAKAAFKTWKEVPVSERARVMLRYQHLLKEHHDE 83 
                                     89***************************************************************************** PP

                       TIGR01722  80 iaklisaeqGktledakGdvarGlevvehacsvtslllGetvesvakdvdvysirqplGvvaGitpfnfpamiplwmfp 158
                                     +a +++ e Gkt+edakGdv+rG+ev ehac+++sll+Getve+va+++d+ys++qplGv+aGitpfnfpamiplwmfp
  lcl|FitnessBrowser__MR1:200843  84 LATILAHETGKTFEDAKGDVWRGIEVAEHACNIASLLMGETVENVARSIDTYSYTQPLGVCAGITPFNFPAMIPLWMFP 162
                                     ******************************************************************************* PP

                       TIGR01722 159 laiacGntfvlkpsekvpsaavklaellseaGapdGvlnvvhGdkeavdrllehpdvkavsfvGsvavgeyiyetgsah 237
                                     laiacGntf+lkpse++p +  +l el+ eaGap+Gvl+++hGdk avd ll  p vka+sfvGsvavg+yiy+tg+ +
  lcl|FitnessBrowser__MR1:200843 163 LAIACGNTFILKPSEQDPMTPQRLVELFVEAGAPKGVLQLIHGDKTAVDILLADPAVKAISFVGSVAVGQYIYKTGTDN 241
                                     ******************************************************************************* PP

                       TIGR01722 238 gkrvqalaGaknhmvvlpdadkeaaldalvgaavGaaGqrcmaisaavlvGaakelveeireraekvrvgagddpgael 316
                                      krvqa+aGaknh v++pda+k++++++lvga+vGaaGqrcmais+av vGaake+++e++e+++kvr+g +dd  a +
  lcl|FitnessBrowser__MR1:200843 242 LKRVQAFAGAKNHCVIMPDANKQQVINNLVGASVGAAGQRCMAISVAVFVGAAKEWIPELKEALAKVRPGLWDDKDAGY 320
                                     ******************************************************************************* PP

                       TIGR01722 317 GplitkqakervasliasgakeGaevlldGrgykveGyeeGnfvGitllervkpdmkiykeeifGpvlvvleadtleea 395
                                     Gpli+++ak rv +lia+g +eGa+ lldG  ++v G+e Gn+vG+t++++v +dm+iykeeifGpvl+ +e+d+le+a
  lcl|FitnessBrowser__MR1:200843 321 GPLISPAAKVRVLKLIAQGKEEGAQCLLDGSDFTVAGFESGNWVGPTMFTKVTTDMSIYKEEIFGPVLCCMESDSLEDA 399
                                     ******************************************************************************* PP

                       TIGR01722 396 iklinespyGnGtaiftsdGaaarkfqheievGqvGvnvpipvplpffsftGwkdslfGdlhiyGkqGvrfytrlktvt 474
                                     i+l+n+spyGnGt+ift++Gaaark+qheievGqvG+nvpipvplpffsftGwk+s++Gd+h+yGkq vrfyt++kt+t
  lcl|FitnessBrowser__MR1:200843 400 IELVNASPYGNGTSIFTASGAAARKYQHEIEVGQVGINVPIPVPLPFFSFTGWKGSFYGDQHAYGKQAVRFYTETKTIT 478
                                     ******************************************************************************* PP

                       TIGR01722 475 arw 477
                                     arw
  lcl|FitnessBrowser__MR1:200843 479 ARW 481
                                     *** PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (477 nodes)
Target sequences:                          1  (499 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: 7.45
//
[ok]

This GapMind analysis is from Sep 17 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 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