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 Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27) (characterized)
to candidate PP_4667 PP_4667 methylmalonate-semialdehyde dehydrogenase

Query= reanno::pseudo13_GW456_L13:PfGW456L13_5146
         (508 letters)



>FitnessBrowser__Putida:PP_4667
          Length = 508

 Score =  903 bits (2334), Expect = 0.0
 Identities = 441/508 (86%), Positives = 477/508 (93%)

Query: 1   MNVSLTPNDTTVQKVKLLIDGQWVESKTTEWHDIINPATQQVLAKVPFATAEEVDAAISA 60
           MN   +PN T V++VKLLIDGQWVESKTTEW DI+NPATQ+VLA+VPFAT EEVDAA++A
Sbjct: 1   MNAPQSPNSTKVEQVKLLIDGQWVESKTTEWRDIVNPATQEVLARVPFATVEEVDAAVAA 60

Query: 61  AHRAFQTWKLTPIGARMRIMLKLQALIREHSKRIAAVLSAEQGKTIADAEGDIFRGLEVV 120
           A RAFQTW+ TPIGARMRIMLKLQALIREH+KRIA VLSAEQGKT+ADAEGDIFRGLEVV
Sbjct: 61  AQRAFQTWRNTPIGARMRIMLKLQALIREHTKRIAQVLSAEQGKTLADAEGDIFRGLEVV 120

Query: 121 EHACSIGSLQMGEFAENVAGGVDTYTLRQPIGVCAGITPFNFPAMIPLWMFPMAIACGNT 180
           EHA SIG+LQMGEFAENVAGGVDTYTLRQPIGVCAGITPFNFPAMIPLWMFPMAI CGNT
Sbjct: 121 EHAASIGTLQMGEFAENVAGGVDTYTLRQPIGVCAGITPFNFPAMIPLWMFPMAIVCGNT 180

Query: 181 FVLKPSEQDPMSTMLLVELAIEAGIPAGVLNVVHGGKDVVDGLCTHKDIKAVSFVGSTAV 240
           FVLKPSEQDP+STMLLVELA+EAG+PAGVLNVVHGGK VVD +CTH+DIKA+SFVGST V
Sbjct: 181 FVLKPSEQDPLSTMLLVELALEAGVPAGVLNVVHGGKQVVDAICTHQDIKAISFVGSTEV 240

Query: 241 GTHVYDLAGKHGKRVQSMMGAKNHAVVLPDANREQALNALVGAGFGAAGQRCMATSVVVL 300
           GTHVY+L  +HGKRVQSMMGAKNHAVVLPDANR Q +NALVGA FGAAGQRCMATSV VL
Sbjct: 241 GTHVYNLGSQHGKRVQSMMGAKNHAVVLPDANRTQTINALVGAAFGAAGQRCMATSVAVL 300

Query: 301 VGAAKQWLPDLKALAQKLKVNAGSEPGTDVGPVISKKAKARILDLIESGIKEGAKLELDG 360
           VG A++WLPD+K  A KLKVNAG EPGTDVGPV+SK+AK R+L LIESGIKEGAKLELDG
Sbjct: 301 VGKAREWLPDIKEAASKLKVNAGCEPGTDVGPVVSKRAKERVLGLIESGIKEGAKLELDG 360

Query: 361 REISVPGYEKGNFVGPTLFSGVTTDMQIYTQEIFGPVLVVLEVNTLDEAIALVNANPFGN 420
           R++ VPGYE+GNFVGPTLFSGV TDMQ+YTQEIFGPVLV LEV+TLDEAIALVNANPFGN
Sbjct: 361 RDVKVPGYEQGNFVGPTLFSGVKTDMQVYTQEIFGPVLVTLEVDTLDEAIALVNANPFGN 420

Query: 421 GTGLFTQSGAAARKFQNEIDVGQVGINIPIPVPVPFFSFTGSRGSKLGDLGPYGKQVVQF 480
           GTGLFTQSGAAARKFQ+EID+GQVGINIPIPVPVPFFSFTGSRGSKLGDLGPYGKQVVQF
Sbjct: 421 GTGLFTQSGAAARKFQSEIDIGQVGINIPIPVPVPFFSFTGSRGSKLGDLGPYGKQVVQF 480

Query: 481 YTQTKTVTSRWFDDDSVNDGVNTTINLR 508
           YTQTKTVT+RWFDDDSVNDGVNTTI+LR
Sbjct: 481 YTQTKTVTARWFDDDSVNDGVNTTISLR 508


Lambda     K      H
   0.318    0.135    0.395 

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: 896
Number of extensions: 27
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: 508
Length of database: 508
Length adjustment: 34
Effective length of query: 474
Effective length of database: 474
Effective search space:   224676
Effective search space used:   224676
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 52 (24.6 bits)

Align candidate PP_4667 PP_4667 (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.29100.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   1.6e-234  764.9   2.6   1.8e-234  764.7   2.6    1.0  1  lcl|FitnessBrowser__Putida:PP_4667  PP_4667 methylmalonate-semialdeh


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Putida:PP_4667  PP_4667 methylmalonate-semialdehyde dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  764.7   2.6  1.8e-234  1.8e-234       1     477 []      15     491 ..      15     491 .. 1.00

  Alignments for each domain:
  == domain 1  score: 764.7 bits;  conditional E-value: 1.8e-234
                           TIGR01722   1 vkhlidGkfvegksdkyipvsnpatnevlakvaeasaeevdaavasaretfaawaetsvaerarvllryqallke 75 
                                         vk+lidG+ ve+k++++ ++ npat+evla+v++a++eevdaava+a+++f++w++t++  r r++l+ qal++e
  lcl|FitnessBrowser__Putida:PP_4667  15 VKLLIDGQWVESKTTEWRDIVNPATQEVLARVPFATVEEVDAAVAAAQRAFQTWRNTPIGARMRIMLKLQALIRE 89 
                                         899************************************************************************ PP

                           TIGR01722  76 hrdeiaklisaeqGktledakGdvarGlevvehacsvtslllGetvesvakdvdvysirqplGvvaGitpfnfpa 150
                                         h + ia+++saeqGktl+da+Gd++rGlevveha s+ +l +Ge  e+va  vd+y++rqp+Gv+aGitpfnfpa
  lcl|FitnessBrowser__Putida:PP_4667  90 HTKRIAQVLSAEQGKTLADAEGDIFRGLEVVEHAASIGTLQMGEFAENVAGGVDTYTLRQPIGVCAGITPFNFPA 164
                                         *************************************************************************** PP

                           TIGR01722 151 miplwmfplaiacGntfvlkpsekvpsaavklaellseaGapdGvlnvvhGdkeavdrllehpdvkavsfvGsva 225
                                         miplwmfp+ai+cGntfvlkpse++p++++ l el +eaG+p GvlnvvhG+k+ vd ++ h d+ka+sfvGs++
  lcl|FitnessBrowser__Putida:PP_4667 165 MIPLWMFPMAIVCGNTFVLKPSEQDPLSTMLLVELALEAGVPAGVLNVVHGGKQVVDAICTHQDIKAISFVGSTE 239
                                         *************************************************************************** PP

                           TIGR01722 226 vgeyiyetgsahgkrvqalaGaknhmvvlpdadkeaaldalvgaavGaaGqrcmaisaavlvGaakelveeirer 300
                                         vg ++y+ gs+hgkrvq+++Gaknh+vvlpda++ ++++alvgaa+GaaGqrcma s+avlvG+a+e++++i+e+
  lcl|FitnessBrowser__Putida:PP_4667 240 VGTHVYNLGSQHGKRVQSMMGAKNHAVVLPDANRTQTINALVGAAFGAAGQRCMATSVAVLVGKAREWLPDIKEA 314
                                         *************************************************************************** PP

                           TIGR01722 301 aekvrvgagddpgaelGplitkqakervasliasgakeGaevlldGrgykveGyeeGnfvGitllervkpdmkiy 375
                                         a k++v+ag +pg+++Gp+++k+akerv  li+sg+keGa++ ldGr +kv Gye+GnfvG+tl+++vk+dm++y
  lcl|FitnessBrowser__Putida:PP_4667 315 ASKLKVNAGCEPGTDVGPVVSKRAKERVLGLIESGIKEGAKLELDGRDVKVPGYEQGNFVGPTLFSGVKTDMQVY 389
                                         *************************************************************************** PP

                           TIGR01722 376 keeifGpvlvvleadtleeaiklinespyGnGtaiftsdGaaarkfqheievGqvGvnvpipvplpffsftGwkd 450
                                          +eifGpvlv le+dtl+eai+l+n++p+GnGt +ft++Gaaarkfq ei++GqvG+n+pipvp+pffsftG+++
  lcl|FitnessBrowser__Putida:PP_4667 390 TQEIFGPVLVTLEVDTLDEAIALVNANPFGNGTGLFTQSGAAARKFQSEIDIGQVGINIPIPVPVPFFSFTGSRG 464
                                         *************************************************************************** PP

                           TIGR01722 451 slfGdlhiyGkqGvrfytrlktvtarw 477
                                         s  Gdl  yGkq v+fyt++ktvtarw
  lcl|FitnessBrowser__Putida:PP_4667 465 SKLGDLGPYGKQVVQFYTQTKTVTARW 491
                                         *************************** PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (477 nodes)
Target sequences:                          1  (508 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 0.02s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 11.03
//
[ok]

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

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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