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 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 5208453 Shew_0965 methylmalonate-semialdehyde dehydrogenase (RefSeq)

Query= BRENDA::A0A081YAY7
         (498 letters)



>FitnessBrowser__PV4:5208453
          Length = 496

 Score =  619 bits (1595), Expect = 0.0
 Identities = 303/496 (61%), Positives = 373/496 (75%), Gaps = 2/496 (0%)

Query: 1   MTLIKHLIGGELIADTGRTADVFNPSTGEAVRKVPLADRETMQQAIDAAKAAFPAWRNTP 60
           M  I H I G+    + R+A VF P+TGE    V LA    +  AI+ AK A   W    
Sbjct: 1   MQQINHYINGQHTQPSARSAAVFEPATGEHKANVSLASALEVDAAIELAKKAHGPWSEMT 60

Query: 61  PAKRAQVLFRFKQLLEANEERIVKLISEEHGKTIEDAAGELKRGIENVEYATAAPEILKG 120
           P  RA++LF+FK L+EAN + +  +I+ EHGK ++DA GE+ RG+E VE+A   P +LKG
Sbjct: 61  PLNRARILFKFKALVEANMDELAAMITREHGKVLDDAKGEIIRGLEVVEFACGIPHLLKG 120

Query: 121 EYSRNVGPNIDAWSDFQPIGVVAGITPFNFPAMVPLWMYPLAIACGNTFILKPSERDPSS 180
           E++  VG  +DAW+  Q +GVVAGI PFNFP MVP+WM+P+AIA GNTFI+KPSE+DP+S
Sbjct: 121 EHTEQVGGGVDAWTLNQSLGVVAGIAPFNFPVMVPMWMFPIAIAAGNTFIMKPSEKDPTS 180

Query: 181 TLLIAELFHEAGLPKGVLNVVHGDKGAVDALIEAPEVKALSFVGSTPIAEYIYSEGTKRG 240
            + +AEL  EAGLP GV NVV+GDK AVD L+   +++A+SFVGSTPIAEYIY      G
Sbjct: 181 VMRMAELLTEAGLPDGVFNVVNGDKEAVDTLLTHKDIQAVSFVGSTPIAEYIYQTAAAHG 240

Query: 241 KRVQALGGAKNHAVLMPDADLDNAVSALMGAAYGSCGERCMAISVAVCVGDQIADALVQK 300
           KRVQALGGAKNH +LMPDADLD AVSALMGAAYGS GERCMAISV + VG ++ DALV+K
Sbjct: 241 KRVQALGGAKNHMLLMPDADLDQAVSALMGAAYGSAGERCMAISVVLAVG-EVGDALVEK 299

Query: 301 LVPQIKGLKIGAGTSCGLDMGPLVTGAARDKVTGYIDTGVAQGAELVVDGRGYKVAGHEN 360
           L+PQI+ LK+G G    ++MGPL++    DKV  Y+DTGV++GA L+ DGR   VA HE 
Sbjct: 300 LLPQIQALKVGNGLEGEMEMGPLISAQHLDKVRSYVDTGVSEGASLLADGRQLTVADHEQ 359

Query: 361 GFFLGGTLFDRVTPEMTIYKEEIFGPVLCIVRVNSLEEAMQLINDHEYGNGTCIFTRDGE 420
           G+FLGG LFD VTPEMTIYKEEIFGPVL IVRV    EA+ LIN+HE+GNGT IFT+ GE
Sbjct: 360 GYFLGGCLFDHVTPEMTIYKEEIFGPVLTIVRVKDYAEALTLINEHEFGNGTAIFTQSGE 419

Query: 421 AARLFCDEIEVGMVGVNVPLPVPVAYHSFGGWKRSLFGDLHAYGPDGVRFYTKRKAITQR 480
           AAR FC  ++VGMVGVNVP+PVP+A+HSFGGWKRSLFG LH +GPDGVRFYTKRKAIT R
Sbjct: 420 AARHFCHHVQVGMVGVNVPIPVPMAFHSFGGWKRSLFGPLHMHGPDGVRFYTKRKAITAR 479

Query: 481 WPQRKSHEAAQFAFPS 496
           WP+ K  + A+F  P+
Sbjct: 480 WPKGKGSQ-AEFVMPT 494


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: 746
Number of extensions: 19
Number of successful extensions: 2
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: 496
Length adjustment: 34
Effective length of query: 464
Effective length of database: 462
Effective search space:   214368
Effective search space used:   214368
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 5208453 Shew_0965 (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.30172.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                        -----------
   2.2e-206  672.0   0.5   2.5e-206  671.9   0.5    1.0  1  lcl|FitnessBrowser__PV4:5208453  Shew_0965 methylmalonate-semiald


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PV4:5208453  Shew_0965 methylmalonate-semialdehyde dehydrogenase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  671.9   0.5  2.5e-206  2.5e-206       1     477 []       4     480 ..       4     480 .. 0.99

  Alignments for each domain:
  == domain 1  score: 671.9 bits;  conditional E-value: 2.5e-206
                        TIGR01722   1 vkhlidGkfvegksdkyipvsnpatnevlakvaeasaeevdaavasaretfaawaetsvaerarvllryqallkehrd 78 
                                      ++h+i+G+  +  s++   v +pat+e  a+v+ asa evdaa+  a++++  w+e + ++rar+l++++al++++ d
  lcl|FitnessBrowser__PV4:5208453   4 INHYINGQHTQ-PSARSAAVFEPATGEHKANVSLASALEVDAAIELAKKAHGPWSEMTPLNRARILFKFKALVEANMD 80 
                                      689****9876.5789999*********************************************************** PP

                        TIGR01722  79 eiaklisaeqGktledakGdvarGlevvehacsvtslllGetvesvakdvdvysirqplGvvaGitpfnfpamiplwm 156
                                      e+a +i+ e+Gk+l+dakG+++rGlevve+ac+++ ll+Ge +e+v   vd ++++q lGvvaGi+pfnfp m+p+wm
  lcl|FitnessBrowser__PV4:5208453  81 ELAAMITREHGKVLDDAKGEIIRGLEVVEFACGIPHLLKGEHTEQVGGGVDAWTLNQSLGVVAGIAPFNFPVMVPMWM 158
                                      ****************************************************************************** PP

                        TIGR01722 157 fplaiacGntfvlkpsekvpsaavklaellseaGapdGvlnvvhGdkeavdrllehpdvkavsfvGsvavgeyiyetg 234
                                      fp+aia Gntf++kpsek+p++ +++aell+eaG+pdGv+nvv Gdkeavd+ll h d++avsfvGs++++eyiy+t+
  lcl|FitnessBrowser__PV4:5208453 159 FPIAIAAGNTFIMKPSEKDPTSVMRMAELLTEAGLPDGVFNVVNGDKEAVDTLLTHKDIQAVSFVGSTPIAEYIYQTA 236
                                      ****************************************************************************** PP

                        TIGR01722 235 sahgkrvqalaGaknhmvvlpdadkeaaldalvgaavGaaGqrcmaisaavlvGaa.kelveeireraekvrvgagdd 311
                                      +ahgkrvqal+Gaknhm+++pdad+++a++al+gaa+G+aG+rcmais++++vG++ + lve++  +++ ++vg g +
  lcl|FitnessBrowser__PV4:5208453 237 AAHGKRVQALGGAKNHMLLMPDADLDQAVSALMGAAYGSAGERCMAISVVLAVGEVgDALVEKLLPQIQALKVGNGLE 314
                                      ********************************************************999******************* PP

                        TIGR01722 312 pgaelGplitkqakervasliasgakeGaevlldGrgykveGyeeGnfvGitllervkpdmkiykeeifGpvlvvlea 389
                                         e+Gpli+ q+ ++v s++++g+ eGa++l dGr ++v  +e+G f+G +l+++v p+m+iykeeifGpvl+++++
  lcl|FitnessBrowser__PV4:5208453 315 GEMEMGPLISAQHLDKVRSYVDTGVSEGASLLADGRQLTVADHEQGYFLGGCLFDHVTPEMTIYKEEIFGPVLTIVRV 392
                                      ****************************************************************************** PP

                        TIGR01722 390 dtleeaiklinespyGnGtaiftsdGaaarkfqheievGqvGvnvpipvplpffsftGwkdslfGdlhiyGkqGvrfy 467
                                        + ea+ line  +GnGtaift++G aar+f h+++vG+vGvnvpipvp++f+sf+Gwk slfG lh++G +Gvrfy
  lcl|FitnessBrowser__PV4:5208453 393 KDYAEALTLINEHEFGNGTAIFTQSGEAARHFCHHVQVGMVGVNVPIPVPMAFHSFGGWKRSLFGPLHMHGPDGVRFY 470
                                      ****************************************************************************** PP

                        TIGR01722 468 trlktvtarw 477
                                      t+ k++tarw
  lcl|FitnessBrowser__PV4:5208453 471 TKRKAITARW 480
                                      ********** PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (477 nodes)
Target sequences:                          1  (496 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 12.36
//
[ok]

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

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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