Alignments for a candidate for mmsA in Pseudomonas fluorescens FW300-N1B4

GapMind for catabolism of small carbon sources

Alignments for a candidate for mmsA in Pseudomonas fluorescens FW300-N1B4

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 Pf1N1B4_1238 Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27)

Query= BRENDA::A0A081YAY7
         (498 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1238
          Length = 497

 Score =  903 bits (2334), Expect = 0.0
 Identities = 440/496 (88%), Positives = 467/496 (94%)

Query: 1   MTLIKHLIGGELIADTGRTADVFNPSTGEAVRKVPLADRETMQQAIDAAKAAFPAWRNTP 60
           M+LI HLI GEL+ + GRTADVFNPSTG+A+ K+PLA RET+Q+AID+AKAAFPAWRNTP
Sbjct: 1   MSLIPHLINGELVTEDGRTADVFNPSTGQAIHKLPLASRETIQKAIDSAKAAFPAWRNTP 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 KRVQALGGAKNHAVLMPDADLDNAVSALMGAAYGSCGERCMAISVAVCVGDQVADALVAK 300

Query: 301 LVPQIKGLKIGAGTSCGLDMGPLVTGAARDKVTGYIDTGVAQGAELVVDGRGYKVAGHEN 360
           LVPQ+K LKIGAGT+CGLDMGPLV+G ARDKV+GYI+ GV+ GA LVVDGRG  VAGHE 
Sbjct: 301 LVPQVKALKIGAGTTCGLDMGPLVSGQARDKVSGYIEDGVSAGATLVVDGRGLSVAGHEE 360

Query: 361 GFFLGGTLFDRVTPEMTIYKEEIFGPVLCIVRVNSLEEAMQLINDHEYGNGTCIFTRDGE 420
           GFFLGG LFD VTPEM IYKEEIFGPVLC+VRVNSLEEAMQLINDHEYGNGTCIFTRDGE
Sbjct: 361 GFFLGGCLFDNVTPEMRIYKEEIFGPVLCVVRVNSLEEAMQLINDHEYGNGTCIFTRDGE 420

Query: 421 AARLFCDEIEVGMVGVNVPLPVPVAYHSFGGWKRSLFGDLHAYGPDGVRFYTKRKAITQR 480
           AARLFCDEIEVGMVGVNVPLPVPVAYHSFGGWKRSLFGDLHAYGPDGVRFYT+RK ITQR
Sbjct: 421 AARLFCDEIEVGMVGVNVPLPVPVAYHSFGGWKRSLFGDLHAYGPDGVRFYTRRKTITQR 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: 913
Number of extensions: 18
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 Pf1N1B4_1238 (Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27))
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.20071.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                      -----------
   2.4e-211  688.4   0.0   2.7e-211  688.2   0.0    1.0  1  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1238  Methylmalonate-semialdehyde dehy


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1238  Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  688.2   0.0  2.7e-211  2.7e-211       3     477 .]       6     481 ..       4     481 .. 0.99

  Alignments for each domain:
  == domain 1  score: 688.2 bits;  conditional E-value: 2.7e-211
                                      TIGR01722   3 hlidGkfvegksdkyipvsnpatnevlakvaeasaeevdaavasaretfaawaetsvaerarvl 66 
                                                    hli+G++v    ++  +v np t++ + k++ as e +++a+ sa+ +f+aw++t+ a+ra+v+
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1238   6 HLINGELVTE-DGRTADVFNPSTGQAIHKLPLASRETIQKAIDSAKAAFPAWRNTPPAKRAQVM 68 
                                                    8999999975.56789************************************************ PP

                                      TIGR01722  67 lryqallkehrdeiaklisaeqGktledakGdvarGlevvehacsvtslllGetvesvakdvdv 130
                                                    +r+++ll++++  ia+lis e+Gktleda G++ rG+e ve+ac+ + +l+Ge + +v  ++d 
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1238  69 FRFKQLLEQNEARIAQLISEEHGKTLEDAAGELKRGIENVEFACAAPEILKGEYSRNVGPNIDA 132
                                                    **************************************************************** PP

                                      TIGR01722 131 ysirqplGvvaGitpfnfpamiplwmfplaiacGntfvlkpsekvpsaavklaellseaGapdG 194
                                                    +s  qplGvvaGitpfnfpam+plwm+plai+cGn+f+lkpse++ps+++ +a+ll+eaG+p+G
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1238 133 WSDFQPLGVVAGITPFNFPAMVPLWMYPLAIVCGNCFILKPSERDPSSTLLIAQLLLEAGLPKG 196
                                                    **************************************************************** PP

                                      TIGR01722 195 vlnvvhGdkeavdrllehpdvkavsfvGsvavgeyiyetgsahgkrvqalaGaknhmvvlpdad 258
                                                    vl vvhGdk avd l+e p+vka+sfvGs++++eyiy  g+++gkrvqal+Gaknh+v++pdad
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1238 197 VLSVVHGDKAAVDALIEAPEVKALSFVGSTPIAEYIYAEGTKRGKRVQALGGAKNHAVLMPDAD 260
                                                    **************************************************************** PP

                                      TIGR01722 259 keaaldalvgaavGaaGqrcmaisaavlvGaa..kelveeireraekvrvgagddpgaelGpli 320
                                                    +++a++al+gaa+G+ G+rcmais+av vG+   + lv +++ +++ +++gag+  g ++Gpl+
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1238 261 LDNAVSALMGAAYGSCGERCMAISVAVCVGDQvaDALVAKLVPQVKALKIGAGTTCGLDMGPLV 324
                                                    ******************************855699**************************** PP

                                      TIGR01722 321 tkqakervasliasgakeGaevlldGrgykveGyeeGnfvGitllervkpdmkiykeeifGpvl 384
                                                    + qa+++v+ +i++g+  Ga +++dGrg+ v G+eeG f+G +l+++v p+m+iykeeifGpvl
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1238 325 SGQARDKVSGYIEDGVSAGATLVVDGRGLSVAGHEEGFFLGGCLFDNVTPEMRIYKEEIFGPVL 388
                                                    **************************************************************** PP

                                      TIGR01722 385 vvleadtleeaiklinespyGnGtaiftsdGaaarkfqheievGqvGvnvpipvplpffsftGw 448
                                                    +v+++++leea++lin+  yGnGt+ift+dG aar f  eievG+vGvnvp+pvp++++sf+Gw
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1238 389 CVVRVNSLEEAMQLINDHEYGNGTCIFTRDGEAARLFCDEIEVGMVGVNVPLPVPVAYHSFGGW 452
                                                    **************************************************************** PP

                                      TIGR01722 449 kdslfGdlhiyGkqGvrfytrlktvtarw 477
                                                    k slfGdlh+yG +Gvrfytr kt+t rw
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1238 453 KRSLFGDLHAYGPDGVRFYTRRKTITQRW 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: 10.86
//
[ok]

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

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