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.26624.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: 7.48
//
[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:

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:

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:

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:

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