Alignments for a candidate for mmsA in Shewanella amazonensis SB2B

GapMind for catabolism of small carbon sources

Alignments for a candidate for mmsA in Shewanella amazonensis SB2B

Align Methylmalonate-semialdehyde dehydrogenase [acylating]; MMSDH; EC 1.2.1.27 (characterized)
to candidate 6937206 Sama_1376 methylmalonate-semialdehyde dehydrogenase (RefSeq)

Query= SwissProt::P28810
         (497 letters)



>FitnessBrowser__SB2B:6937206
          Length = 497

 Score =  752 bits (1942), Expect = 0.0
 Identities = 363/497 (73%), Positives = 412/497 (82%)

Query: 1   MSVPVRHLIAGAFVEGLGAQRIPVSNPLDNSTLAEIACASAEQVEQAVASARETFASWKE 60
           M   V+H I G F  G G + I V+NP +N  +AE+ CAS E+V  A+ASA+  F SWKE
Sbjct: 1   MITQVKHYIDGEFTTGQGERIITVTNPANNQPIAEVRCASDEEVHGAIASAKAAFQSWKE 60

Query: 61  TPVSERARVMLRYQALLKEHHDELAKIVSSELGKTFEDAKGDVWRGIEVVEHACNVPSLL 120
            PVSERARVMLRYQALLKEHHDELA I++ E GKTFEDAKGDVWRGIEV EHACN+ SLL
Sbjct: 61  VPVSERARVMLRYQALLKEHHDELATILAKETGKTFEDAKGDVWRGIEVAEHACNIASLL 120

Query: 121 MGETVENVARNIDTYSITQPLGVCVGITPFNFPAMIPLWMFPLAIACGNAFILKPSEQVP 180
           MGETVENVAR IDTYS TQPLGVC GITPFNFPAMIPLWMFPLA+ACGN F+LKPSEQ P
Sbjct: 121 MGETVENVARKIDTYSYTQPLGVCAGITPFNFPAMIPLWMFPLAVACGNTFVLKPSEQDP 180

Query: 181 LTSVRLAELFLEAGAPKGVLQVVHGGKEQVDQLLKHPQVKAVSFVGSVAVGQYVYHTGTA 240
           +T +RLAELF +AGAPKGVLQ+VHG K  VD LL HP +KA+SFVGSV VGQYVY TGT 
Sbjct: 181 MTPLRLAELFEQAGAPKGVLQLVHGDKSAVDILLTHPDIKAISFVGSVGVGQYVYKTGTD 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 AKAR+ +LI QG  EGA+ LLDG  + V GY  
Sbjct: 301 LKEALAKVRPGLWDDKDAGYGPLISPAAKARVLKLIEQGKAEGAECLLDGSDFTVPGYES 360

Query: 361 GNWVGPTLFAGVRPDMAIYREEVFGPVLCLAEVDSLEQAIRLINESPYGNGTSIFTSSGA 420
           GNWVGPT+F  V  DM+IY+EE+FGPVLC  EVD LE AI L+N+SPYGNGTSIFT+SGA
Sbjct: 361 GNWVGPTMFDKVTTDMSIYKEEIFGPVLCCMEVDELEDAIELVNKSPYGNGTSIFTASGA 420

Query: 421 AARTFQHHIEVGQVGINIPIPVPLPFFSFTGWKGSFYGDLHAYGKQGVRFYTETKTVTAR 480
           AAR +QH IEVGQVGIN+PIPVPLPFFSFTGWKGSFYGD HAYGKQ +RF+TETKT+T R
Sbjct: 421 AARKYQHEIEVGQVGINVPIPVPLPFFSFTGWKGSFYGDQHAYGKQAIRFFTETKTITCR 480

Query: 481 WFDSDSVAGTNFSIQMR 497
           WF+ D   G N +I +R
Sbjct: 481 WFEDDIPHGPNMTIALR 497


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: 864
Number of extensions: 35
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: 497
Length adjustment: 34
Effective length of query: 463
Effective length of database: 463
Effective search space:   214369
Effective search space used:   214369
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 6937206 Sama_1376 (methylmalonate-semialdehyde dehydrogenase (RefSeq))
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.21017.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   2.9e-253  826.7   0.2   3.2e-253  826.5   0.2    1.0  1  lcl|FitnessBrowser__SB2B:6937206  Sama_1376 methylmalonate-semiald


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__SB2B:6937206  Sama_1376 methylmalonate-semialdehyde dehydrogenase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  826.5   0.2  3.2e-253  3.2e-253       1     477 []       5     481 ..       5     481 .. 1.00

  Alignments for each domain:
  == domain 1  score: 826.5 bits;  conditional E-value: 3.2e-253
                         TIGR01722   1 vkhlidGkfvegksdkyipvsnpatnevlakvaeasaeevdaavasaretfaawaetsvaerarvllryqallkehr 77 
                                       vkh+idG+f  g++++ i v+npa+n+ +a+v +as eev+ a+asa+ +f++w+e +v+erarv+lryqallkeh+
  lcl|FitnessBrowser__SB2B:6937206   5 VKHYIDGEFTTGQGERIITVTNPANNQPIAEVRCASDEEVHGAIASAKAAFQSWKEVPVSERARVMLRYQALLKEHH 81 
                                       89*************************************************************************** PP

                         TIGR01722  78 deiaklisaeqGktledakGdvarGlevvehacsvtslllGetvesvakdvdvysirqplGvvaGitpfnfpamipl 154
                                       de+a +++ e Gkt+edakGdv+rG+ev ehac+++sll+Getve+va+++d+ys++qplGv+aGitpfnfpamipl
  lcl|FitnessBrowser__SB2B:6937206  82 DELATILAKETGKTFEDAKGDVWRGIEVAEHACNIASLLMGETVENVARKIDTYSYTQPLGVCAGITPFNFPAMIPL 158
                                       ***************************************************************************** PP

                         TIGR01722 155 wmfplaiacGntfvlkpsekvpsaavklaellseaGapdGvlnvvhGdkeavdrllehpdvkavsfvGsvavgeyiy 231
                                       wmfpla+acGntfvlkpse++p + ++lael+++aGap+Gvl++vhGdk avd ll hpd+ka+sfvGsv vg+y+y
  lcl|FitnessBrowser__SB2B:6937206 159 WMFPLAVACGNTFVLKPSEQDPMTPLRLAELFEQAGAPKGVLQLVHGDKSAVDILLTHPDIKAISFVGSVGVGQYVY 235
                                       ***************************************************************************** PP

                         TIGR01722 232 etgsahgkrvqalaGaknhmvvlpdadkeaaldalvgaavGaaGqrcmaisaavlvGaakelveeireraekvrvga 308
                                       +tg+ + krvqa+aGaknh v++pda+k++++++lvga+vGaaGqrcmais+av vGaake+++e++e+++kvr+g 
  lcl|FitnessBrowser__SB2B:6937206 236 KTGTDNLKRVQAFAGAKNHCVIMPDANKQQVINNLVGASVGAAGQRCMAISVAVFVGAAKEWIPELKEALAKVRPGL 312
                                       ***************************************************************************** PP

                         TIGR01722 309 gddpgaelGplitkqakervasliasgakeGaevlldGrgykveGyeeGnfvGitllervkpdmkiykeeifGpvlv 385
                                       +dd  a +Gpli+++ak+rv +li++g +eGae lldG  ++v Gye Gn+vG+t++++v +dm+iykeeifGpvl+
  lcl|FitnessBrowser__SB2B:6937206 313 WDDKDAGYGPLISPAAKARVLKLIEQGKAEGAECLLDGSDFTVPGYESGNWVGPTMFDKVTTDMSIYKEEIFGPVLC 389
                                       ***************************************************************************** PP

                         TIGR01722 386 vleadtleeaiklinespyGnGtaiftsdGaaarkfqheievGqvGvnvpipvplpffsftGwkdslfGdlhiyGkq 462
                                        +e+d le+ai+l+n+spyGnGt+ift++Gaaark+qheievGqvG+nvpipvplpffsftGwk+s++Gd+h+yGkq
  lcl|FitnessBrowser__SB2B:6937206 390 CMEVDELEDAIELVNKSPYGNGTSIFTASGAAARKYQHEIEVGQVGINVPIPVPLPFFSFTGWKGSFYGDQHAYGKQ 466
                                       ***************************************************************************** PP

                         TIGR01722 463 Gvrfytrlktvtarw 477
                                        +rf+t++kt+t+rw
  lcl|FitnessBrowser__SB2B:6937206 467 AIRFFTETKTITCRW 481
                                       *************** PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (477 nodes)
Target sequences:                          1  (497 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: 00:00:00.02
# Mc/sec: 10.86
//
[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