GapMind for catabolism of small carbon sources

 

Aligments for a candidate for mmsA in Pseudomonas simiae WCS417

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 GFF640 PS417_03250 methylmalonate-semialdehyde dehydrogenase

Query= BRENDA::A0A081YAY7
         (498 letters)



>lcl|FitnessBrowser__WCS417:GFF640 PS417_03250
           methylmalonate-semialdehyde dehydrogenase
          Length = 498

 Score =  911 bits (2354), Expect = 0.0
 Identities = 445/498 (89%), Positives = 471/498 (94%)

Query: 1   MTLIKHLIGGELIADTGRTADVFNPSTGEAVRKVPLADRETMQQAIDAAKAAFPAWRNTP 60
           M+LI+HLI GEL+ D+GR+ADV+NPSTG+ + +VPLA RET+QQAID+AKAAFPAWRNTP
Sbjct: 1   MSLIQHLINGELVNDSGRSADVYNPSTGQVIHQVPLASRETIQQAIDSAKAAFPAWRNTP 60

Query: 61  PAKRAQVLFRFKQLLEANEERIVKLISEEHGKTIEDAAGELKRGIENVEYATAAPEILKG 120
            AKRAQV+FRFKQLLE NE RI +LISEEHGKT+EDAAGELKRGIENVEYA +APEILKG
Sbjct: 61  AAKRAQVMFRFKQLLEQNEARISQLISEEHGKTLEDAAGELKRGIENVEYACSAPEILKG 120

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

Query: 181 TLLIAELFHEAGLPKGVLNVVHGDKGAVDALIEAPEVKALSFVGSTPIAEYIYSEGTKRG 240
           TLLIA+L  EAGLPKGVL+VVHGDKGAVDALIEAPEVKALSFVGSTPIAEYIYSE TKRG
Sbjct: 181 TLLIAQLLQEAGLPKGVLSVVHGDKGAVDALIEAPEVKALSFVGSTPIAEYIYSEATKRG 240

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

Query: 301 LVPQIKGLKIGAGTSCGLDMGPLVTGAARDKVTGYIDTGVAQGAELVVDGRGYKVAGHEN 360
           LVPQ+K LKIGAGTSCGLDMGPLVTG ARDKV+GYID GVA GAELVVDGRG  VAGHE 
Sbjct: 301 LVPQVKALKIGAGTSCGLDMGPLVTGQARDKVSGYIDDGVAAGAELVVDGRGLSVAGHEE 360

Query: 361 GFFLGGTLFDRVTPEMTIYKEEIFGPVLCIVRVNSLEEAMQLINDHEYGNGTCIFTRDGE 420
           GFFLGG+LFDRVTPEM IYKEEIFGPVLC+VRVNSLE AMQLINDHEYGNGTCIFTRDGE
Sbjct: 361 GFFLGGSLFDRVTPEMRIYKEEIFGPVLCVVRVNSLEAAMQLINDHEYGNGTCIFTRDGE 420

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

Query: 481 WPQRKSHEAAQFAFPSNS 498
           WPQR SHEA+QFAFPS S
Sbjct: 481 WPQRASHEASQFAFPSLS 498


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: 918
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: 498
Length adjustment: 34
Effective length of query: 464
Effective length of database: 464
Effective search space:   215296
Effective search space used:   215296
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 GFF640 PS417_03250 (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.27735.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
     3e-214  698.0   0.0   3.4e-214  697.8   0.0    1.0  1  lcl|FitnessBrowser__WCS417:GFF640  PS417_03250 methylmalonate-semia


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__WCS417:GFF640  PS417_03250 methylmalonate-semialdehyde dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  697.8   0.0  3.4e-214  3.4e-214       1     477 []       4     481 ..       4     481 .. 0.99

  Alignments for each domain:
  == domain 1  score: 697.8 bits;  conditional E-value: 3.4e-214
                          TIGR01722   1 vkhlidGkfvegksdkyipvsnpatnevlakvaeasaeevdaavasaretfaawaetsvaerarvllryqallkeh 76 
                                        ++hli+G++v+  s++  +v np t++v+ +v+ as e +++a+ sa+ +f+aw++t+ a+ra+v++r+++ll+++
  lcl|FitnessBrowser__WCS417:GFF640   4 IQHLINGELVND-SGRSADVYNPSTGQVIHQVPLASRETIQQAIDSAKAAFPAWRNTPAAKRAQVMFRFKQLLEQN 78 
                                        589*****9975.78899********************************************************** PP

                          TIGR01722  77 rdeiaklisaeqGktledakGdvarGlevvehacsvtslllGetvesvakdvdvysirqplGvvaGitpfnfpami 152
                                        +  i++lis e+Gktleda G++ rG+e ve+acs + +l+Ge + +v  ++d +s  qplGvvaGitpfnfpam+
  lcl|FitnessBrowser__WCS417:GFF640  79 EARISQLISEEHGKTLEDAAGELKRGIENVEYACSAPEILKGEYSRNVGPNIDAWSDFQPLGVVAGITPFNFPAMV 154
                                        **************************************************************************** PP

                          TIGR01722 153 plwmfplaiacGntfvlkpsekvpsaavklaellseaGapdGvlnvvhGdkeavdrllehpdvkavsfvGsvavge 228
                                        plwm+plai+cGn+f+lkpse++ps+++ +a+ll+eaG+p+Gvl vvhGdk avd l+e p+vka+sfvGs++++e
  lcl|FitnessBrowser__WCS417:GFF640 155 PLWMYPLAIVCGNCFILKPSERDPSSTLLIAQLLQEAGLPKGVLSVVHGDKGAVDALIEAPEVKALSFVGSTPIAE 230
                                        **************************************************************************** PP

                          TIGR01722 229 yiyetgsahgkrvqalaGaknhmvvlpdadkeaaldalvgaavGaaGqrcmaisaavlvGaa..kelveeirerae 302
                                        yiy+ ++++gkrvqal+Gaknh+v++pdad+++a++al+gaa+G+ G+rcmais+av vG+   + l+ +++ +++
  lcl|FitnessBrowser__WCS417:GFF640 231 YIYSEATKRGKRVQALGGAKNHAVLMPDADLDNAVSALMGAAYGSCGERCMAISVAVCVGDQvaDALIAKLVPQVK 306
                                        ************************************************************855699********** PP

                          TIGR01722 303 kvrvgagddpgaelGplitkqakervasliasgakeGaevlldGrgykveGyeeGnfvGitllervkpdmkiykee 378
                                         +++gag+  g ++Gpl+t qa+++v+ +i++g++ Gae+++dGrg+ v G+eeG f+G +l++rv p+m+iykee
  lcl|FitnessBrowser__WCS417:GFF640 307 ALKIGAGTSCGLDMGPLVTGQARDKVSGYIDDGVAAGAELVVDGRGLSVAGHEEGFFLGGSLFDRVTPEMRIYKEE 382
                                        **************************************************************************** PP

                          TIGR01722 379 ifGpvlvvleadtleeaiklinespyGnGtaiftsdGaaarkfqheievGqvGvnvpipvplpffsftGwkdslfG 454
                                        ifGpvl+v+++++le a++lin+  yGnGt+ift+dG aar f  eievG+vGvnvp+pvp++++sf+Gwk slfG
  lcl|FitnessBrowser__WCS417:GFF640 383 IFGPVLCVVRVNSLEAAMQLINDHEYGNGTCIFTRDGEAARLFCDEIEVGMVGVNVPLPVPVAYHSFGGWKRSLFG 458
                                        **************************************************************************** PP

                          TIGR01722 455 dlhiyGkqGvrfytrlktvtarw 477
                                        dlh+yG +Gvrfytr k++t rw
  lcl|FitnessBrowser__WCS417:GFF640 459 DLHAYGPDGVRFYTRRKAITQRW 481
                                        *********************** PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (477 nodes)
Target sequences:                          1  (498 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: 00:00:00.03
# Mc/sec: 7.39
//
[ok]

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

Links

Downloads

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 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