Alignments for a candidate for mmsA in Pseudomonas fluorescens FW300-N2E3

GapMind for catabolism of small carbon sources

Alignments for a candidate for mmsA in Pseudomonas fluorescens FW300-N2E3

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 AO353_06080 AO353_06080 methylmalonate-semialdehyde dehydrogenase

Query= BRENDA::A0A081YAY7
         (498 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_06080
          Length = 497

 Score =  903 bits (2334), Expect = 0.0
 Identities = 442/496 (89%), Positives = 465/496 (93%)

Query: 1   MTLIKHLIGGELIADTGRTADVFNPSTGEAVRKVPLADRETMQQAIDAAKAAFPAWRNTP 60
           M+LI HLI GEL+ D  RTADVFNPSTG+ + KVPLA RET+Q+AID+AKAAFPAWRNTP
Sbjct: 1   MSLIPHLINGELVTDNARTADVFNPSTGQPIHKVPLASRETIQKAIDSAKAAFPAWRNTP 60

Query: 61  PAKRAQVLFRFKQLLEANEERIVKLISEEHGKTIEDAAGELKRGIENVEYATAAPEILKG 120
           PAKRAQV+FRFKQLLE NE RI +LISEEHGKT+EDAAGELKRGIENVE+A AAPEILKG
Sbjct: 61  PAKRAQVMFRFKQLLEQNEARIAQLISEEHGKTLEDAAGELKRGIENVEFACAAPEILKG 120

Query: 121 EYSRNVGPNIDAWSDFQPIGVVAGITPFNFPAMVPLWMYPLAIACGNTFILKPSERDPSS 180
           EYSRNVGPNIDAWSDFQP+GVVAGITPFNFPAMVPLWMYPLAI CGN FILKPSERDPSS
Sbjct: 121 EYSRNVGPNIDAWSDFQPLGVVAGITPFNFPAMVPLWMYPLAIVCGNCFILKPSERDPSS 180

Query: 181 TLLIAELFHEAGLPKGVLNVVHGDKGAVDALIEAPEVKALSFVGSTPIAEYIYSEGTKRG 240
           TLLIA+L  EAGLPKGVL+VVHGDK AVDALIEAPEVKALSFVGSTPIAEYIY+EGTKRG
Sbjct: 181 TLLIAQLLLEAGLPKGVLSVVHGDKAAVDALIEAPEVKALSFVGSTPIAEYIYAEGTKRG 240

Query: 241 KRVQALGGAKNHAVLMPDADLDNAVSALMGAAYGSCGERCMAISVAVCVGDQIADALVQK 300
           KRVQALGGAKNHAVLMPDADLDNAVSALMGAAYGSCGERCMAISVAVCVGDQ+ADALV K
Sbjct: 241 KRVQALGGAKNHAVLMPDADLDNAVSALMGAAYGSCGERCMAISVAVCVGDQVADALVTK 300

Query: 301 LVPQIKGLKIGAGTSCGLDMGPLVTGAARDKVTGYIDTGVAQGAELVVDGRGYKVAGHEN 360
           LVPQIK LKIGAGTSCGLDMGPLV+G ARDKV+GYI+ GV+ GA L+VDGRG  VAGHE 
Sbjct: 301 LVPQIKALKIGAGTSCGLDMGPLVSGQARDKVSGYIEDGVSAGASLIVDGRGLSVAGHEE 360

Query: 361 GFFLGGTLFDRVTPEMTIYKEEIFGPVLCIVRVNSLEEAMQLINDHEYGNGTCIFTRDGE 420
           GFFLGG LFD VTPEM IYKEEIFGPVLCIVRVNSLE AMQLINDHEYGNGTCIFTRDGE
Sbjct: 361 GFFLGGCLFDNVTPEMRIYKEEIFGPVLCIVRVNSLEAAMQLINDHEYGNGTCIFTRDGE 420

Query: 421 AARLFCDEIEVGMVGVNVPLPVPVAYHSFGGWKRSLFGDLHAYGPDGVRFYTKRKAITQR 480
           AARLFCDEIEVGMVGVNVPLPVPVAYHSFGGWKRSLFGDLHAYGPDGVRFYT+RKAITQR
Sbjct: 421 AARLFCDEIEVGMVGVNVPLPVPVAYHSFGGWKRSLFGDLHAYGPDGVRFYTRRKAITQR 480

Query: 481 WPQRKSHEAAQFAFPS 496
           WPQR SHEA+QFAFPS
Sbjct: 481 WPQRASHEASQFAFPS 496


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: 903
Number of extensions: 17
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: 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 AO353_06080 AO353_06080 (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.3627.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                     -----------
   2.5e-210  685.1   0.0   2.8e-210  684.9   0.0    1.0  1  lcl|FitnessBrowser__pseudo3_N2E3:AO353_06080  AO353_06080 methylmalonate-semia


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo3_N2E3:AO353_06080  AO353_06080 methylmalonate-semialdehyde dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  684.9   0.0  2.8e-210  2.8e-210       3     477 .]       6     481 ..       4     481 .. 0.99

  Alignments for each domain:
  == domain 1  score: 684.9 bits;  conditional E-value: 2.8e-210
                                     TIGR01722   3 hlidGkfvegksdkyipvsnpatnevlakvaeasaeevdaavasaretfaawaetsvaerarvll 67 
                                                   hli+G++v   +++  +v np t++ + kv+ as e +++a+ sa+ +f+aw++t+ a+ra+v++
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_06080   6 HLINGELVTD-NARTADVFNPSTGQPIHKVPLASRETIQKAIDSAKAAFPAWRNTPPAKRAQVMF 69 
                                                   8999999976.56789************************************************* PP

                                     TIGR01722  68 ryqallkehrdeiaklisaeqGktledakGdvarGlevvehacsvtslllGetvesvakdvdvys 132
                                                   r+++ll++++  ia+lis e+Gktleda G++ rG+e ve+ac+ + +l+Ge + +v  ++d +s
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_06080  70 RFKQLLEQNEARIAQLISEEHGKTLEDAAGELKRGIENVEFACAAPEILKGEYSRNVGPNIDAWS 134
                                                   ***************************************************************** PP

                                     TIGR01722 133 irqplGvvaGitpfnfpamiplwmfplaiacGntfvlkpsekvpsaavklaellseaGapdGvln 197
                                                     qplGvvaGitpfnfpam+plwm+plai+cGn+f+lkpse++ps+++ +a+ll+eaG+p+Gvl 
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_06080 135 DFQPLGVVAGITPFNFPAMVPLWMYPLAIVCGNCFILKPSERDPSSTLLIAQLLLEAGLPKGVLS 199
                                                   ***************************************************************** PP

                                     TIGR01722 198 vvhGdkeavdrllehpdvkavsfvGsvavgeyiyetgsahgkrvqalaGaknhmvvlpdadkeaa 262
                                                   vvhGdk avd l+e p+vka+sfvGs++++eyiy  g+++gkrvqal+Gaknh+v++pdad+++a
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_06080 200 VVHGDKAAVDALIEAPEVKALSFVGSTPIAEYIYAEGTKRGKRVQALGGAKNHAVLMPDADLDNA 264
                                                   ***************************************************************** PP

                                     TIGR01722 263 ldalvgaavGaaGqrcmaisaavlvGaa..kelveeireraekvrvgagddpgaelGplitkqak 325
                                                   ++al+gaa+G+ G+rcmais+av vG+   + lv +++ +++ +++gag+  g ++Gpl++ qa+
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_06080 265 VSALMGAAYGSCGERCMAISVAVCVGDQvaDALVTKLVPQIKALKIGAGTSCGLDMGPLVSGQAR 329
                                                   **************************855699********************************* PP

                                     TIGR01722 326 ervasliasgakeGaevlldGrgykveGyeeGnfvGitllervkpdmkiykeeifGpvlvvlead 390
                                                   ++v+ +i++g+  Ga++++dGrg+ v G+eeG f+G +l+++v p+m+iykeeifGpvl++++++
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_06080 330 DKVSGYIEDGVSAGASLIVDGRGLSVAGHEEGFFLGGCLFDNVTPEMRIYKEEIFGPVLCIVRVN 394
                                                   ***************************************************************** PP

                                     TIGR01722 391 tleeaiklinespyGnGtaiftsdGaaarkfqheievGqvGvnvpipvplpffsftGwkdslfGd 455
                                                   +le a++lin+  yGnGt+ift+dG aar f  eievG+vGvnvp+pvp++++sf+Gwk slfGd
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_06080 395 SLEAAMQLINDHEYGNGTCIFTRDGEAARLFCDEIEVGMVGVNVPLPVPVAYHSFGGWKRSLFGD 459
                                                   ***************************************************************** PP

                                     TIGR01722 456 lhiyGkqGvrfytrlktvtarw 477
                                                   lh+yG +Gvrfytr k++t rw
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_06080 460 LHAYGPDGVRFYTRRKAITQRW 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 9.92
//
[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