Alignments for a candidate for mmsA in Herbaspirillum seropedicae SmR1

GapMind for catabolism of small carbon sources

Alignments for a candidate for mmsA in Herbaspirillum seropedicae SmR1

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 HSERO_RS23245 HSERO_RS23245 methylmalonate-semialdehyde dehydrogenase

Query= BRENDA::A0A081YAY7
         (498 letters)



>FitnessBrowser__HerbieS:HSERO_RS23245
          Length = 497

 Score =  627 bits (1618), Expect = 0.0
 Identities = 310/496 (62%), Positives = 375/496 (75%), Gaps = 3/496 (0%)

Query: 1   MTLIKHLIGGELI-ADTGRTADVFNPSTGEAVRKVPLADRETMQQAIDAAKAAFPAWRNT 59
           M  I H IGG+ +   +GR ADVFNP+ G  V +V L   + +  A+ A  AAFPAW NT
Sbjct: 1   MEKIAHYIGGQRVDTRSGRYADVFNPAQGVPVAQVALGTSDEVDAAVKAGVAAFPAWSNT 60

Query: 60  PPAKRAQVLFRFKQLLEANEERIVKLISEEHGKTIEDAAGELKRGIENVEYATAAPEILK 119
           PP  RA+VLFRF  L++   +   ++I  EHGKT  DA GE+ RGIE VE+A   P++LK
Sbjct: 61  PPLTRARVLFRFLHLIQQRADDFARIIVREHGKTFSDAQGEVARGIEIVEFAAGIPQMLK 120

Query: 120 GEYSRNVGPNIDAWSDFQPIGVVAGITPFNFPAMVPLWMYPLAIACGNTFILKPSERDPS 179
           GEY+  +   IDAWS  Q +GVVAGITPFNFPAMVP+WM+P+AIACGN F+LKPSERDPS
Sbjct: 121 GEYTDQIARGIDAWSMRQALGVVAGITPFNFPAMVPMWMFPIAIACGNCFVLKPSERDPS 180

Query: 180 STLLIAELFHEAGLPKGVLNVVHGDKGAVDALIEAPEVKALSFVGSTPIAEYIYSEGTKR 239
           ++LLIA+L  EAGLP GV NVV GDK  VDAL++ P+VKA+SFVGSTPIAEYIY+ G+ +
Sbjct: 181 ASLLIADLLKEAGLPDGVFNVVQGDKVTVDALLDHPQVKAISFVGSTPIAEYIYARGSAK 240

Query: 240 GKRVQALGGAKNHAVLMPDADLDNAVSALMGAAYGSCGERCMAISVAVCVGDQIADALVQ 299
           GKRVQALGGAKNH V+MPDAD+  AV ALMGAAYGS GERCMAISVA+ VG    D LV 
Sbjct: 241 GKRVQALGGAKNHMVVMPDADMQLAVDALMGAAYGSAGERCMAISVALAVG-SAGDELVA 299

Query: 300 KLVPQIKGLKIGAGTSCGLDMGPLVTGAARDKVTGYIDTGVAQGAELVVDGRGYKVAGHE 359
            L  + + LKI  G + G +MGP+VT AA++++ G I  GV +GA LVVDGRGY+V G E
Sbjct: 300 ALAERARKLKINEGMAAGAEMGPVVTAAAKERIEGLIGRGVEEGATLVVDGRGYQVPGFE 359

Query: 360 NGFFLGGTLFDRVTPEMTIYKEEIFGPVLCIVRVNSLEEAMQLINDHEYGNGTCIFTRDG 419
            GFF+GGTL D VTPEMT+YKEEIFGPVLC++R   +  A++LIN HEYGNG  ++TRDG
Sbjct: 360 KGFFVGGTLLDHVTPEMTVYKEEIFGPVLCVLRCPDIASAVELINAHEYGNGVAVYTRDG 419

Query: 420 EAARLFCDEIEVGMVGVNVPLPVPVAYHSFGGWKRSLFGDLHAYGPDGVRFYTKRKAITQ 479
             AR F  +IEVGMVGVNVPLPVP+A+ SFGGWKRSLFGD H YGP+GVRFYT+ KA+ Q
Sbjct: 420 GVAREFVRQIEVGMVGVNVPLPVPMAFSSFGGWKRSLFGDHHMYGPEGVRFYTRAKAVMQ 479

Query: 480 RWPQRKSHEAAQFAFP 495
           RWP   S   A+FAFP
Sbjct: 480 RWPNTAS-AGAEFAFP 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: 785
Number of extensions: 22
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: 497
Length adjustment: 34
Effective length of query: 464
Effective length of database: 463
Effective search space:   214832
Effective search space used:   214832
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 HSERO_RS23245 HSERO_RS23245 (methylmalonate-semialdehyde dehydrogenase)
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.22312.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                              -----------
   4.2e-219  714.0   1.7   4.8e-219  713.8   1.7    1.0  1  FitnessBrowser__HerbieS:HSERO_RS23245  


Domain annotation for each sequence (and alignments):
>> FitnessBrowser__HerbieS:HSERO_RS23245  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  713.8   1.7  4.8e-219  4.8e-219       2     477 .]       5     481 ..       4     481 .. 1.00

  Alignments for each domain:
  == domain 1  score: 713.8 bits;  conditional E-value: 4.8e-219
                              TIGR01722   2 khlidGkfvegksdkyipvsnpatnevlakvaeasaeevdaavasaretfaawaetsvaerarvllryqall 73 
                                             h+i+G+ v+++s++y +v npa++  +a+va  + +evdaav +   +f+aw++t+ + rarvl+r+  l+
  FitnessBrowser__HerbieS:HSERO_RS23245   5 AHYIGGQRVDTRSGRYADVFNPAQGVPVAQVALGTSDEVDAAVKAGVAAFPAWSNTPPLTRARVLFRFLHLI 76 
                                            69********************************************************************** PP

                              TIGR01722  74 kehrdeiaklisaeqGktledakGdvarGlevvehacsvtslllGetvesvakdvdvysirqplGvvaGitp 145
                                            +++ d+ a++i+ e+Gkt++da+G+varG+e+ve+a +++ +l+Ge ++++a+ +d +s+rq lGvvaGitp
  FitnessBrowser__HerbieS:HSERO_RS23245  77 QQRADDFARIIVREHGKTFSDAQGEVARGIEIVEFAAGIPQMLKGEYTDQIARGIDAWSMRQALGVVAGITP 148
                                            ************************************************************************ PP

                              TIGR01722 146 fnfpamiplwmfplaiacGntfvlkpsekvpsaavklaellseaGapdGvlnvvhGdkeavdrllehpdvka 217
                                            fnfpam+p+wmfp+aiacGn+fvlkpse++psa++ +a+ll+eaG+pdGv+nvv Gdk++vd ll+hp+vka
  FitnessBrowser__HerbieS:HSERO_RS23245 149 FNFPAMVPMWMFPIAIACGNCFVLKPSERDPSASLLIADLLKEAGLPDGVFNVVQGDKVTVDALLDHPQVKA 220
                                            ************************************************************************ PP

                              TIGR01722 218 vsfvGsvavgeyiyetgsahgkrvqalaGaknhmvvlpdadkeaaldalvgaavGaaGqrcmaisaavlvGa 289
                                            +sfvGs++++eyiy +gsa+gkrvqal+Gaknhmvv+pdad + a+dal+gaa+G+aG+rcmais+a++vG+
  FitnessBrowser__HerbieS:HSERO_RS23245 221 ISFVGSTPIAEYIYARGSAKGKRVQALGGAKNHMVVMPDADMQLAVDALMGAAYGSAGERCMAISVALAVGS 292
                                            ************************************************************************ PP

                              TIGR01722 290 a.kelveeireraekvrvgagddpgaelGplitkqakervasliasgakeGaevlldGrgykveGyeeGnfv 360
                                            a +elv  + era+k++++ g  +gae+Gp++t +aker++ li+ g++eGa +++dGrgy+v G+e+G fv
  FitnessBrowser__HerbieS:HSERO_RS23245 293 AgDELVAALAERARKLKINEGMAAGAEMGPVVTAAAKERIEGLIGRGVEEGATLVVDGRGYQVPGFEKGFFV 364
                                            99********************************************************************** PP

                              TIGR01722 361 GitllervkpdmkiykeeifGpvlvvleadtleeaiklinespyGnGtaiftsdGaaarkfqheievGqvGv 432
                                            G tll++v p+m++ykeeifGpvl+vl++  +  a++lin+  yGnG a++t+dG+ ar+f  +ievG+vGv
  FitnessBrowser__HerbieS:HSERO_RS23245 365 GGTLLDHVTPEMTVYKEEIFGPVLCVLRCPDIASAVELINAHEYGNGVAVYTRDGGVAREFVRQIEVGMVGV 436
                                            ************************************************************************ PP

                              TIGR01722 433 nvpipvplpffsftGwkdslfGdlhiyGkqGvrfytrlktvtarw 477
                                            nvp+pvp++f sf+Gwk slfGd+h+yG +Gvrfytr+k+v  rw
  FitnessBrowser__HerbieS:HSERO_RS23245 437 NVPLPVPMAFSSFGGWKRSLFGDHHMYGPEGVRFYTRAKAVMQRW 481
                                            ********************************************9 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 22.08
//
[ok]

This GapMind analysis is from Apr 09 2024. 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 2024 update 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