Alignments for a candidate for mmsA in Pseudomonas putida KT2440

GapMind for catabolism of small carbon sources

Alignments for a candidate for mmsA in Pseudomonas putida KT2440

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 PP_0597 PP_0597 methylmalonate-semialdehyde dehydrogenase

Query= BRENDA::A0A081YAY7
         (498 letters)



>FitnessBrowser__Putida:PP_0597
          Length = 497

 Score =  898 bits (2320), Expect = 0.0
 Identities = 436/496 (87%), Positives = 470/496 (94%)

Query: 1   MTLIKHLIGGELIADTGRTADVFNPSTGEAVRKVPLADRETMQQAIDAAKAAFPAWRNTP 60
           M++++HLI GEL+    RTADVFNPSTG+AVRKV LA R T+Q+AID+AKAAFPAWRNTP
Sbjct: 1   MSIVQHLIHGELVTKGERTADVFNPSTGQAVRKVELASRATVQEAIDSAKAAFPAWRNTP 60

Query: 61  PAKRAQVLFRFKQLLEANEERIVKLISEEHGKTIEDAAGELKRGIENVEYATAAPEILKG 120
           PAKRAQV+FRFKQLLE NE +I ++ISEEHGKT+EDAAGELKRGIENVE+A AAPE+LKG
Sbjct: 61  PAKRAQVMFRFKQLLEQNEAKISQMISEEHGKTLEDAAGELKRGIENVEFACAAPEVLKG 120

Query: 121 EYSRNVGPNIDAWSDFQPIGVVAGITPFNFPAMVPLWMYPLAIACGNTFILKPSERDPSS 180
           EYSRNVGPNIDAWSDFQP+GVVAGITPFNFPAMVPLWMYPLAIACGN FILKPSERDPSS
Sbjct: 121 EYSRNVGPNIDAWSDFQPLGVVAGITPFNFPAMVPLWMYPLAIACGNAFILKPSERDPSS 180

Query: 181 TLLIAELFHEAGLPKGVLNVVHGDKGAVDALIEAPEVKALSFVGSTPIAEYIYSEGTKRG 240
           TL IA+L  EAGLPKG+LNVVHGDK AVDALIEAPEVKALSFVGSTPIAEYIY+EGTKRG
Sbjct: 181 TLYIAQLLLEAGLPKGILNVVHGDKEAVDALIEAPEVKALSFVGSTPIAEYIYAEGTKRG 240

Query: 241 KRVQALGGAKNHAVLMPDADLDNAVSALMGAAYGSCGERCMAISVAVCVGDQIADALVQK 300
           KRVQALGGAKNHAVLMPDADLDNAVSALMGAAYGSCGERCMAISVAVCVGDQ+ADAL+ K
Sbjct: 241 KRVQALGGAKNHAVLMPDADLDNAVSALMGAAYGSCGERCMAISVAVCVGDQVADALIAK 300

Query: 301 LVPQIKGLKIGAGTSCGLDMGPLVTGAARDKVTGYIDTGVAQGAELVVDGRGYKVAGHEN 360
           L PQIK LKIGAGTSCGLDMGPLVT AARDKV GYID GVA GA+LVVDGRG++VAG+E+
Sbjct: 301 LEPQIKALKIGAGTSCGLDMGPLVTAAARDKVVGYIDDGVAAGAKLVVDGRGFRVAGNED 360

Query: 361 GFFLGGTLFDRVTPEMTIYKEEIFGPVLCIVRVNSLEEAMQLINDHEYGNGTCIFTRDGE 420
           G+F+GGTLFD+VTPEM IYKEEIFGPVLC+VRVNSLE+AMQLINDHEYGNGTCIFTRDGE
Sbjct: 361 GYFVGGTLFDKVTPEMRIYKEEIFGPVLCVVRVNSLEQAMQLINDHEYGNGTCIFTRDGE 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: 882
Number of extensions: 16
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 PP_0597 PP_0597 (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.26417.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   4.4e-213  694.1   0.1     5e-213  694.0   0.1    1.0  1  lcl|FitnessBrowser__Putida:PP_0597  PP_0597 methylmalonate-semialdeh


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Putida:PP_0597  PP_0597 methylmalonate-semialdehyde dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  694.0   0.1    5e-213    5e-213       1     477 []       4     481 ..       4     481 .. 0.99

  Alignments for each domain:
  == domain 1  score: 694.0 bits;  conditional E-value: 5e-213
                           TIGR01722   1 vkhlidGkfvegksdkyipvsnpatnevlakvaeasaeevdaavasaretfaawaetsvaerarvllryqallke 75 
                                         v+hli G++v +k+++  +v np t++ + kv  as + v++a+ sa+ +f+aw++t+ a+ra+v++r+++ll++
  lcl|FitnessBrowser__Putida:PP_0597   4 VQHLIHGELV-TKGERTADVFNPSTGQAVRKVELASRATVQEAIDSAKAAFPAWRNTPPAKRAQVMFRFKQLLEQ 77 
                                         79******98.6899************************************************************ PP

                           TIGR01722  76 hrdeiaklisaeqGktledakGdvarGlevvehacsvtslllGetvesvakdvdvysirqplGvvaGitpfnfpa 150
                                         ++ +i+++is e+Gktleda G++ rG+e ve+ac+ +  l+Ge + +v  ++d +s  qplGvvaGitpfnfpa
  lcl|FitnessBrowser__Putida:PP_0597  78 NEAKISQMISEEHGKTLEDAAGELKRGIENVEFACAAPEVLKGEYSRNVGPNIDAWSDFQPLGVVAGITPFNFPA 152
                                         *************************************************************************** PP

                           TIGR01722 151 miplwmfplaiacGntfvlkpsekvpsaavklaellseaGapdGvlnvvhGdkeavdrllehpdvkavsfvGsva 225
                                         m+plwm+plaiacGn+f+lkpse++ps+++ +a+ll+eaG+p+G+lnvvhGdkeavd l+e p+vka+sfvGs++
  lcl|FitnessBrowser__Putida:PP_0597 153 MVPLWMYPLAIACGNAFILKPSERDPSSTLYIAQLLLEAGLPKGILNVVHGDKEAVDALIEAPEVKALSFVGSTP 227
                                         *************************************************************************** PP

                           TIGR01722 226 vgeyiyetgsahgkrvqalaGaknhmvvlpdadkeaaldalvgaavGaaGqrcmaisaavlvGaa..kelveeir 298
                                         ++eyiy  g+++gkrvqal+Gaknh+v++pdad+++a++al+gaa+G+ G+rcmais+av vG+   + l+ ++ 
  lcl|FitnessBrowser__Putida:PP_0597 228 IAEYIYAEGTKRGKRVQALGGAKNHAVLMPDADLDNAVSALMGAAYGSCGERCMAISVAVCVGDQvaDALIAKLE 302
                                         ***************************************************************855699****** PP

                           TIGR01722 299 eraekvrvgagddpgaelGplitkqakervasliasgakeGaevlldGrgykveGyeeGnfvGitllervkpdmk 373
                                          +++ +++gag+  g ++Gpl+t +a+++v  +i++g++ Ga++++dGrg++v G e+G fvG tl+++v p+m+
  lcl|FitnessBrowser__Putida:PP_0597 303 PQIKALKIGAGTSCGLDMGPLVTAAARDKVVGYIDDGVAAGAKLVVDGRGFRVAGNEDGYFVGGTLFDKVTPEMR 377
                                         *************************************************************************** PP

                           TIGR01722 374 iykeeifGpvlvvleadtleeaiklinespyGnGtaiftsdGaaarkfqheievGqvGvnvpipvplpffsftGw 448
                                         iykeeifGpvl+v+++++le+a++lin+  yGnGt+ift+dG aar f  eievG+vGvnvp+pvp++++sf+Gw
  lcl|FitnessBrowser__Putida:PP_0597 378 IYKEEIFGPVLCVVRVNSLEQAMQLINDHEYGNGTCIFTRDGEAARLFCDEIEVGMVGVNVPLPVPVAYHSFGGW 452
                                         *************************************************************************** PP

                           TIGR01722 449 kdslfGdlhiyGkqGvrfytrlktvtarw 477
                                         k slfGdlh+yG +Gvrfytr k++t rw
  lcl|FitnessBrowser__Putida:PP_0597 453 KRSLFGDLHAYGPDGVRFYTRRKAITQRW 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 9.78
//
[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