Alignments for a candidate for mmsA in Shewanella loihica PV-4

GapMind for catabolism of small carbon sources

Alignments for a candidate for mmsA in Shewanella loihica PV-4

Align Methylmalonate-semialdehyde dehydrogenase [acylating]; MMSDH; EC 1.2.1.27 (characterized)
to candidate 5209190 Shew_1668 methylmalonate-semialdehyde dehydrogenase (RefSeq)

Query= SwissProt::P28810
         (497 letters)



>FitnessBrowser__PV4:5209190
          Length = 501

 Score =  748 bits (1932), Expect = 0.0
 Identities = 359/496 (72%), Positives = 415/496 (83%)

Query: 1   MSVPVRHLIAGAFVEGLGAQRIPVSNPLDNSTLAEIACASAEQVEQAVASARETFASWKE 60
           M+  V+H I G F+ G G Q+I V+NP +N  +A I  A+ E+VE A+ASA++ FA+WKE
Sbjct: 1   MTTQVKHYIDGQFILGSGQQQISVTNPANNEVIATINAATVEEVETAIASAKQAFATWKE 60

Query: 61  TPVSERARVMLRYQALLKEHHDELAKIVSSELGKTFEDAKGDVWRGIEVVEHACNVPSLL 120
            PVSERARVM RYQ LLK HHDE+A I++ E GKTFEDAKGDVWRGIEV EHACN+ SL+
Sbjct: 61  VPVSERARVMFRYQHLLKLHHDEIATILAQETGKTFEDAKGDVWRGIEVAEHACNIASLI 120

Query: 121 MGETVENVARNIDTYSITQPLGVCVGITPFNFPAMIPLWMFPLAIACGNAFILKPSEQVP 180
           MGETVENVAR+IDTYS TQPLGVC GITPFNFPAMIPLWMFPLAIACGN F+LKPSEQ P
Sbjct: 121 MGETVENVARSIDTYSYTQPLGVCAGITPFNFPAMIPLWMFPLAIACGNTFVLKPSEQDP 180

Query: 181 LTSVRLAELFLEAGAPKGVLQVVHGGKEQVDQLLKHPQVKAVSFVGSVAVGQYVYHTGTA 240
           LT  RL ELF EAGAPKGVLQ+VHG K  VD LL H  +KA+SFVGSV VGQY+Y TGT 
Sbjct: 181 LTPQRLVELFEEAGAPKGVLQLVHGDKTAVDVLLSHQDIKAISFVGSVGVGQYIYKTGTD 240

Query: 241 HNKRVQSFAGAKNHMVIMPDADKAQVISNLVGASVGAAGQRCMAISVAVLVGAAREWIPE 300
           + KRVQ+FAGAKNH VIMPDA+K QVI+NLVGASVGAAGQRCMA+SVAV VG A++WIPE
Sbjct: 241 NLKRVQAFAGAKNHCVIMPDANKQQVINNLVGASVGAAGQRCMALSVAVFVGEAKKWIPE 300

Query: 301 IRDALAKVRPGPWDDSGASYGPVINPQAKARIERLIGQGVEEGAQLLLDGRGYKVEGYPD 360
           +RDA+AKVRPG WDD  A+YGPVI+P AKAR+ +LI QG EEGA+ LLDG  + VEGY +
Sbjct: 301 LRDAIAKVRPGVWDDKDAAYGPVISPAAKARVLKLIAQGKEEGAECLLDGSDFTVEGYEN 360

Query: 361 GNWVGPTLFAGVRPDMAIYREEVFGPVLCLAEVDSLEQAIRLINESPYGNGTSIFTSSGA 420
           GNWVGPT+F  V  DM+IY+EE+FGPVLC  EV+SLE+AI L+N SPYGNGTSIFT+ GA
Sbjct: 361 GNWVGPTMFTNVTTDMSIYKEEIFGPVLCCMEVESLEEAIELVNNSPYGNGTSIFTACGA 420

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

Query: 481 WFDSDSVAGTNFSIQM 496
           WF++D V   + +  M
Sbjct: 481 WFETDIVEAEHHAPNM 496


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: 808
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: 501
Length adjustment: 34
Effective length of query: 463
Effective length of database: 467
Effective search space:   216221
Effective search space used:   216221
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 5209190 Shew_1668 (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.12343.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                        -----------
   1.5e-254  830.9   1.8   1.7e-254  830.7   1.8    1.0  1  lcl|FitnessBrowser__PV4:5209190  Shew_1668 methylmalonate-semiald


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PV4:5209190  Shew_1668 methylmalonate-semialdehyde dehydrogenase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  830.7   1.8  1.7e-254  1.7e-254       1     477 []       5     481 ..       5     481 .. 1.00

  Alignments for each domain:
  == domain 1  score: 830.7 bits;  conditional E-value: 1.7e-254
                        TIGR01722   1 vkhlidGkfvegksdkyipvsnpatnevlakvaeasaeevdaavasaretfaawaetsvaerarvllryqallkehrd 78 
                                      vkh+idG+f+ g +++ i v+npa+nev+a +  a++eev++a+asa+++fa+w+e +v+erarv++ryq llk h+d
  lcl|FitnessBrowser__PV4:5209190   5 VKHYIDGQFILGSGQQQISVTNPANNEVIATINAATVEEVETAIASAKQAFATWKEVPVSERARVMFRYQHLLKLHHD 82 
                                      89**************************************************************************** PP

                        TIGR01722  79 eiaklisaeqGktledakGdvarGlevvehacsvtslllGetvesvakdvdvysirqplGvvaGitpfnfpamiplwm 156
                                      eia +++ e Gkt+edakGdv+rG+ev ehac+++sl++Getve+va+++d+ys++qplGv+aGitpfnfpamiplwm
  lcl|FitnessBrowser__PV4:5209190  83 EIATILAQETGKTFEDAKGDVWRGIEVAEHACNIASLIMGETVENVARSIDTYSYTQPLGVCAGITPFNFPAMIPLWM 160
                                      ****************************************************************************** PP

                        TIGR01722 157 fplaiacGntfvlkpsekvpsaavklaellseaGapdGvlnvvhGdkeavdrllehpdvkavsfvGsvavgeyiyetg 234
                                      fplaiacGntfvlkpse++p++  +l el++eaGap+Gvl++vhGdk avd ll h d+ka+sfvGsv vg+yiy+tg
  lcl|FitnessBrowser__PV4:5209190 161 FPLAIACGNTFVLKPSEQDPLTPQRLVELFEEAGAPKGVLQLVHGDKTAVDVLLSHQDIKAISFVGSVGVGQYIYKTG 238
                                      ****************************************************************************** PP

                        TIGR01722 235 sahgkrvqalaGaknhmvvlpdadkeaaldalvgaavGaaGqrcmaisaavlvGaakelveeireraekvrvgagddp 312
                                      + + krvqa+aGaknh v++pda+k++++++lvga+vGaaGqrcma+s+av vG+ak++++e+r++++kvr+g +dd 
  lcl|FitnessBrowser__PV4:5209190 239 TDNLKRVQAFAGAKNHCVIMPDANKQQVINNLVGASVGAAGQRCMALSVAVFVGEAKKWIPELRDAIAKVRPGVWDDK 316
                                      ****************************************************************************** PP

                        TIGR01722 313 gaelGplitkqakervasliasgakeGaevlldGrgykveGyeeGnfvGitllervkpdmkiykeeifGpvlvvlead 390
                                       a +Gp+i+++ak+rv +lia+g +eGae lldG  ++veGye+Gn+vG+t++++v +dm+iykeeifGpvl+ +e++
  lcl|FitnessBrowser__PV4:5209190 317 DAAYGPVISPAAKARVLKLIAQGKEEGAECLLDGSDFTVEGYENGNWVGPTMFTNVTTDMSIYKEEIFGPVLCCMEVE 394
                                      ****************************************************************************** PP

                        TIGR01722 391 tleeaiklinespyGnGtaiftsdGaaarkfqheievGqvGvnvpipvplpffsftGwkdslfGdlhiyGkqGvrfyt 468
                                      +leeai+l+n+spyGnGt+ift+ Gaaark+qh+ievGqvG+nvpipvplpffsftGwk+s++Gd+h+yGkq vrfyt
  lcl|FitnessBrowser__PV4:5209190 395 SLEEAIELVNNSPYGNGTSIFTACGAAARKYQHNIEVGQVGINVPIPVPLPFFSFTGWKGSFYGDQHAYGKQAVRFYT 472
                                      ****************************************************************************** PP

                        TIGR01722 469 rlktvtarw 477
                                      ++kt+tarw
  lcl|FitnessBrowser__PV4:5209190 473 ETKTITARW 481
                                      ********* PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (477 nodes)
Target sequences:                          1  (501 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 0.01s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 11.08
//
[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