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_RS24005 HSERO_RS24005 methylmalonate-semialdehyde dehydrogenase

Query= BRENDA::A0A081YAY7
         (498 letters)



>FitnessBrowser__HerbieS:HSERO_RS24005
          Length = 503

 Score =  611 bits (1576), Expect = e-179
 Identities = 305/497 (61%), Positives = 374/497 (75%), Gaps = 7/497 (1%)

Query: 4   IKHLIGGELI-ADTGRTADVFNPSTGEAVRKVPLADRETMQQAIDAAKAAFPAWRNTPPA 62
           I H I G++  +++GR+ DVFNP+TG A  KV LA  + +  A+ AA AA PAW  T P 
Sbjct: 6   IDHFINGQISRSESGRSQDVFNPATGAATAKVALASVQEVNAAVAAASAAAPAWAETAPL 65

Query: 63  KRAQVLFRFKQLLEANEERIVKLISEEHGKTIEDAAGELKRGIENVEYATAAPEILKGEY 122
           KRA+VLF+FK+L+E N + + K I+ EHGK   DA GE+ RG+E VE+AT  P++LK ++
Sbjct: 66  KRARVLFKFKELIEQNHDALAKAITLEHGKVFSDAKGEVTRGLEIVEFATGIPQLLKTQF 125

Query: 123 SRNVGPNIDAWSDFQPIGVVAGITPFNFPAMVPLWMYPLAIACGNTFILKPSERDPSSTL 182
           + N+G  ID W+  QP+GV AGITPFNFP MVPLWM P+AIA GN+F+LKPSERDPS +L
Sbjct: 126 TDNIGGGIDNWNLRQPLGVTAGITPFNFPVMVPLWMAPIAIATGNSFVLKPSERDPSPSL 185

Query: 183 LIAELFHEAGLPKGVLNVVHGDKGAVDALIEAPEVKALSFVGSTPIAEYIYSEGTKRG-- 240
           ++AELF  AGLP GV NVV GDK AVDAL+E PEV+A+SFVGSTPIAEYIY + T+R   
Sbjct: 186 MLAELFKRAGLPDGVFNVVQGDKVAVDALLEHPEVQAVSFVGSTPIAEYIYRKATERAGT 245

Query: 241 --KRVQALGGAKNHAVLMPDADLDNAVSALMGAAYGSCGERCMAISVAVCVGDQIADALV 298
              R QALGGAKNH V+MPDA+LD AV AL+GAAYGS GERCMAISVAV VG  +AD LV
Sbjct: 246 FPLRAQALGGAKNHLVVMPDANLDQAVDALIGAAYGSAGERCMAISVAVAVG-SVADKLV 304

Query: 299 QKLVPQIKGLKIGAGTSCGLDMGPLVTGAARDKVTGYIDTGVAQGAELVVDGRGYKVAGH 358
           + L+P++K LK+  G     +MGPLVT A + KV GYI +GV  GA+L+VDGRG KV GH
Sbjct: 305 EALIPRVKALKVKNGMEDDAEMGPLVTAAHKAKVEGYIQSGVDAGAKLLVDGRGLKVPGH 364

Query: 359 ENGFFLGGTLFDRVTPEMTIYKEEIFGPVLCIVRVNSLEEAMQLINDHEYGNGTCIFTRD 418
           E GFF+GGTLFD VT EM IY+EEIFGPVLC+VRV     A+QLIN HEYGNG  +FT D
Sbjct: 365 EEGFFIGGTLFDHVTTEMKIYQEEIFGPVLCVVRVPDFASAVQLINAHEYGNGVSLFTAD 424

Query: 419 GEAARLFCDEIEVGMVGVNVPLPVPVAYHSFGGWKRSLFGDLHAYGPDGVRFYTKRKAIT 478
           G  A  F   I+VGMVG+NVP+PVP+A+HSFGGWKRSLFGD HAYG +G+RFYT+ K+I 
Sbjct: 425 GNTAHEFSRRIQVGMVGINVPIPVPMAWHSFGGWKRSLFGDTHAYGEEGIRFYTRYKSIM 484

Query: 479 QRWPQRKSHEAAQFAFP 495
           QRW      + A+F  P
Sbjct: 485 QRW-SATIGKGAEFTMP 500


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: 768
Number of extensions: 27
Number of successful extensions: 3
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: 503
Length adjustment: 34
Effective length of query: 464
Effective length of database: 469
Effective search space:   217616
Effective search space used:   217616
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_RS24005 HSERO_RS24005 (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.22909.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
   8.6e-207  673.4   1.0   9.7e-207  673.2   1.0    1.0  1  lcl|FitnessBrowser__HerbieS:HSERO_RS24005  HSERO_RS24005 methylmalonate-sem


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__HerbieS:HSERO_RS24005  HSERO_RS24005 methylmalonate-semialdehyde dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  673.2   1.0  9.7e-207  9.7e-207       2     477 .]       7     487 ..       6     487 .. 0.99

  Alignments for each domain:
  == domain 1  score: 673.2 bits;  conditional E-value: 9.7e-207
                                  TIGR01722   2 khlidGkfvegksdkyipvsnpatnevlakvaeasaeevdaavasaretfaawaetsvaerarvllry 69 
                                                 h+i+G++  ++s++  +v npat+  +akva as++ev+aava+a  + +awaet+ ++rarvl+++
  lcl|FitnessBrowser__HerbieS:HSERO_RS24005   7 DHFINGQISRSESGRSQDVFNPATGAATAKVALASVQEVNAAVAAASAAAPAWAETAPLKRARVLFKF 74 
                                                79****************************************************************** PP

                                  TIGR01722  70 qallkehrdeiaklisaeqGktledakGdvarGlevvehacsvtslllGetvesvakdvdvysirqpl 137
                                                ++l+++++d +ak i++e+Gk+++dakG+v rGle+ve+a +++ ll+ + ++++   +d + +rqpl
  lcl|FitnessBrowser__HerbieS:HSERO_RS24005  75 KELIEQNHDALAKAITLEHGKVFSDAKGEVTRGLEIVEFATGIPQLLKTQFTDNIGGGIDNWNLRQPL 142
                                                ******************************************************************** PP

                                  TIGR01722 138 GvvaGitpfnfpamiplwmfplaiacGntfvlkpsekvpsaavklaellseaGapdGvlnvvhGdkea 205
                                                Gv+aGitpfnfp m+plwm p+aia Gn+fvlkpse++ps ++ lael++ aG+pdGv+nvv Gdk+a
  lcl|FitnessBrowser__HerbieS:HSERO_RS24005 143 GVTAGITPFNFPVMVPLWMAPIAIATGNSFVLKPSERDPSPSLMLAELFKRAGLPDGVFNVVQGDKVA 210
                                                ******************************************************************** PP

                                  TIGR01722 206 vdrllehpdvkavsfvGsvavgeyiyetgsahgk....rvqalaGaknhmvvlpdadkeaaldalvga 269
                                                vd llehp+v+avsfvGs++++eyiy++++ ++     r qal+Gaknh vv+pda++++a+dal+ga
  lcl|FitnessBrowser__HerbieS:HSERO_RS24005 211 VDALLEHPEVQAVSFVGSTPIAEYIYRKATERAGtfplRAQALGGAKNHLVVMPDANLDQAVDALIGA 278
                                                **************************9998765323449***************************** PP

                                  TIGR01722 270 avGaaGqrcmaisaavlvGaa.kelveeireraekvrvgagddpgaelGplitkqakervasliasga 336
                                                a+G+aG+rcmais+av+vG++ ++lve +  r++ ++v  g +  ae+Gpl+t ++k++v+ +i+sg+
  lcl|FitnessBrowser__HerbieS:HSERO_RS24005 279 AYGSAGERCMAISVAVAVGSVaDKLVEALIPRVKALKVKNGMEDDAEMGPLVTAAHKAKVEGYIQSGV 346
                                                *******************9989********************************************* PP

                                  TIGR01722 337 keGaevlldGrgykveGyeeGnfvGitllervkpdmkiykeeifGpvlvvleadtleeaiklinespy 404
                                                + Ga++l+dGrg+kv G+eeG f+G tl+++v ++mkiy+eeifGpvl+v+++  +  a++lin+  y
  lcl|FitnessBrowser__HerbieS:HSERO_RS24005 347 DAGAKLLVDGRGLKVPGHEEGFFIGGTLFDHVTTEMKIYQEEIFGPVLCVVRVPDFASAVQLINAHEY 414
                                                ******************************************************************** PP

                                  TIGR01722 405 GnGtaiftsdGaaarkfqheievGqvGvnvpipvplpffsftGwkdslfGdlhiyGkqGvrfytrlkt 472
                                                GnG ++ft+dG +a +f+ +i+vG+vG+nvpipvp++++sf+Gwk slfGd+h+yG++G+rfytr k 
  lcl|FitnessBrowser__HerbieS:HSERO_RS24005 415 GNGVSLFTADGNTAHEFSRRIQVGMVGINVPIPVPMAWHSFGGWKRSLFGDTHAYGEEGIRFYTRYKS 482
                                                ******************************************************************** PP

                                  TIGR01722 473 vtarw 477
                                                +  rw
  lcl|FitnessBrowser__HerbieS:HSERO_RS24005 483 IMQRW 487
                                                ****9 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (477 nodes)
Target sequences:                          1  (503 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: 11.23
//
[ok]

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

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Protein sequences (fasta format)
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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