GapMind for catabolism of small carbon sources

 

Aligments for a candidate for mmsA in Pseudomonas simiae WCS417

Align Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27) (characterized)
to candidate GFF4637 PS417_23725 methylmalonate-semialdehyde dehydrogenase

Query= reanno::pseudo1_N1B4:Pf1N1B4_1229
         (505 letters)



>lcl|FitnessBrowser__WCS417:GFF4637 PS417_23725
           methylmalonate-semialdehyde dehydrogenase
          Length = 505

 Score =  944 bits (2441), Expect = 0.0
 Identities = 471/505 (93%), Positives = 493/505 (97%)

Query: 1   MNASLETTVQKVKLLIDGEWVESQTTEWHDIVNPATQQVLAKVPFATAAEVDAAISAAHR 60
           MNAS + +VQ+VKLLI+GEWVES+TTEW DIVNPATQ+VLAKVPFATA EV+AAI AAHR
Sbjct: 1   MNASADISVQQVKLLINGEWVESKTTEWQDIVNPATQEVLAKVPFATADEVNAAIDAAHR 60

Query: 61  AFQTWKLTPIGARMRIMLKLQALIREHSKRIAVVLSNEQGKTIADAEGDIFRGLEVVEHA 120
           AFQTWKLTPIGARMRIMLKLQALIREHSKRIAVVLSNEQGKTIADAEGDIFRGLEVVEHA
Sbjct: 61  AFQTWKLTPIGARMRIMLKLQALIREHSKRIAVVLSNEQGKTIADAEGDIFRGLEVVEHA 120

Query: 121 CSIGSLQMGEFAENVAGGVDTYTLRQPIGVCAGITPFNFPAMIPLWMFPMAIACGNTFVL 180
           CSIG+LQMGEF+ENVAGGVDTYTLRQPIGVCAGITPFNFPAMIPLWMFPMAIACGNTFVL
Sbjct: 121 CSIGTLQMGEFSENVAGGVDTYTLRQPIGVCAGITPFNFPAMIPLWMFPMAIACGNTFVL 180

Query: 181 KPSEQDPMSTMLLVELAIEAGIPPGVLNVVHGGKDVVDALCTHKDIKAVSFVGSTAVGTH 240
           KPSEQDP+STMLLVELA+EAG+P GVLNVVHGGKDVVDALCTHKDIKAVSFVGSTAVGTH
Sbjct: 181 KPSEQDPLSTMLLVELALEAGVPAGVLNVVHGGKDVVDALCTHKDIKAVSFVGSTAVGTH 240

Query: 241 VYDLAGKHGKRVQSMMGAKNHAVVLPDANREQALNALVGAGFGAAGQRCMATSVVVLVGA 300
           VYDLAGKHGKRVQSMMGAKNHAVVLPDANRE  LNALVGAGFGAAGQRCMATSVVVLVGA
Sbjct: 241 VYDLAGKHGKRVQSMMGAKNHAVVLPDANREHTLNALVGAGFGAAGQRCMATSVVVLVGA 300

Query: 301 AKQWLPDLKALAQKLKVNAGSEPGTDVGPVISKRAKARILDLIESGIKEGAKLELDGRDI 360
           +KQWLPDLKALAQKLKVNAGSE GTDVGPVISKRAKARIL+LIESG+KEGAKLELDGRDI
Sbjct: 301 SKQWLPDLKALAQKLKVNAGSEAGTDVGPVISKRAKARILELIESGVKEGAKLELDGRDI 360

Query: 361 SVPGYEKGNFVGPTLFSGVTPEMQIYTQEIFGPVLVVLEVDTLDQAIALVNANPFGNGTG 420
            VPG+E+GNFVGPTLFSGVTP MQIYTQEIFGPVLVVLEV TLD+AIALVNANPFGNGTG
Sbjct: 361 KVPGFEQGNFVGPTLFSGVTPSMQIYTQEIFGPVLVVLEVATLDEAIALVNANPFGNGTG 420

Query: 421 LFTQSGAAARKFQTEIDVGQVGINIPIPVPVPFFSFTGSRGSKLGDLGPYGKQVVQFYTQ 480
           LFTQSGAAARKFQ+EIDVGQVGINIPIPVPVPFFSFTGSRGSKLGDLGPYGKQVVQFYTQ
Sbjct: 421 LFTQSGAAARKFQSEIDVGQVGINIPIPVPVPFFSFTGSRGSKLGDLGPYGKQVVQFYTQ 480

Query: 481 TKTVTARWFDDDSVNDGVNTTIHLR 505
           TKTVT+RWFDDD+VNDGVNTTI+LR
Sbjct: 481 TKTVTSRWFDDDTVNDGVNTTINLR 505


Lambda     K      H
   0.319    0.135    0.397 

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: 923
Number of extensions: 22
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: 505
Length of database: 505
Length adjustment: 34
Effective length of query: 471
Effective length of database: 471
Effective search space:   221841
Effective search space used:   221841
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 GFF4637 PS417_23725 (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.26560.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-229  748.3   2.1   1.9e-229  748.2   2.1    1.0  1  lcl|FitnessBrowser__WCS417:GFF4637  PS417_23725 methylmalonate-semia


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__WCS417:GFF4637  PS417_23725 methylmalonate-semialdehyde dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  748.2   2.1  1.9e-229  1.9e-229       1     477 []      12     488 ..      12     488 .. 1.00

  Alignments for each domain:
  == domain 1  score: 748.2 bits;  conditional E-value: 1.9e-229
                           TIGR01722   1 vkhlidGkfvegksdkyipvsnpatnevlakvaeasaeevdaavasaretfaawaetsvaerarvllryqallke 75 
                                         vk+li+G+ ve+k++++ ++ npat+evlakv++a+a+ev+aa+ +a+++f++w+ t++  r r++l+ qal++e
  lcl|FitnessBrowser__WCS417:GFF4637  12 VKLLINGEWVESKTTEWQDIVNPATQEVLAKVPFATADEVNAAIDAAHRAFQTWKLTPIGARMRIMLKLQALIRE 86 
                                         899************************************************************************ PP

                           TIGR01722  76 hrdeiaklisaeqGktledakGdvarGlevvehacsvtslllGetvesvakdvdvysirqplGvvaGitpfnfpa 150
                                         h + ia ++s eqGkt++da+Gd++rGlevvehacs+ +l +Ge +e+va  vd+y++rqp+Gv+aGitpfnfpa
  lcl|FitnessBrowser__WCS417:GFF4637  87 HSKRIAVVLSNEQGKTIADAEGDIFRGLEVVEHACSIGTLQMGEFSENVAGGVDTYTLRQPIGVCAGITPFNFPA 161
                                         *************************************************************************** PP

                           TIGR01722 151 miplwmfplaiacGntfvlkpsekvpsaavklaellseaGapdGvlnvvhGdkeavdrllehpdvkavsfvGsva 225
                                         miplwmfp+aiacGntfvlkpse++p++++ l el +eaG+p GvlnvvhG+k+ vd l+ h d+kavsfvGs+a
  lcl|FitnessBrowser__WCS417:GFF4637 162 MIPLWMFPMAIACGNTFVLKPSEQDPLSTMLLVELALEAGVPAGVLNVVHGGKDVVDALCTHKDIKAVSFVGSTA 236
                                         *************************************************************************** PP

                           TIGR01722 226 vgeyiyetgsahgkrvqalaGaknhmvvlpdadkeaaldalvgaavGaaGqrcmaisaavlvGaakelveeirer 300
                                         vg ++y+ + +hgkrvq+++Gaknh+vvlpda++e++l+alvga +GaaGqrcma s++vlvGa k+++++++  
  lcl|FitnessBrowser__WCS417:GFF4637 237 VGTHVYDLAGKHGKRVQSMMGAKNHAVVLPDANREHTLNALVGAGFGAAGQRCMATSVVVLVGASKQWLPDLKAL 311
                                         *************************************************************************** PP

                           TIGR01722 301 aekvrvgagddpgaelGplitkqakervasliasgakeGaevlldGrgykveGyeeGnfvGitllervkpdmkiy 375
                                         a+k++v+ag+++g+++Gp+i+k+ak+r+ +li+sg+keGa++ ldGr +kv G+e+GnfvG+tl+++v p+m+iy
  lcl|FitnessBrowser__WCS417:GFF4637 312 AQKLKVNAGSEAGTDVGPVISKRAKARILELIESGVKEGAKLELDGRDIKVPGFEQGNFVGPTLFSGVTPSMQIY 386
                                         *************************************************************************** PP

                           TIGR01722 376 keeifGpvlvvleadtleeaiklinespyGnGtaiftsdGaaarkfqheievGqvGvnvpipvplpffsftGwkd 450
                                          +eifGpvlvvle+ tl+eai+l+n++p+GnGt +ft++Gaaarkfq ei+vGqvG+n+pipvp+pffsftG+++
  lcl|FitnessBrowser__WCS417:GFF4637 387 TQEIFGPVLVVLEVATLDEAIALVNANPFGNGTGLFTQSGAAARKFQSEIDVGQVGINIPIPVPVPFFSFTGSRG 461
                                         *************************************************************************** PP

                           TIGR01722 451 slfGdlhiyGkqGvrfytrlktvtarw 477
                                         s  Gdl  yGkq v+fyt++ktvt+rw
  lcl|FitnessBrowser__WCS417:GFF4637 462 SKLGDLGPYGKQVVQFYTQTKTVTSRW 488
                                         *************************** PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (477 nodes)
Target sequences:                          1  (505 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 7.46
//
[ok]

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

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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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

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:

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. Gaps may be due to:

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 preprint on GapMind for carbon sources, or view the source code.

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