GapMind for catabolism of small carbon sources

 

Aligments for a candidate for mmsA in Pseudomonas fluorescens GW456-L13

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 PfGW456L13_2 Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27)

Query= BRENDA::A0A081YAY7
         (498 letters)



>lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2
           Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27)
          Length = 497

 Score =  902 bits (2331), Expect = 0.0
 Identities = 441/496 (88%), Positives = 465/496 (93%)

Query: 1   MTLIKHLIGGELIADTGRTADVFNPSTGEAVRKVPLADRETMQQAIDAAKAAFPAWRNTP 60
           M++I HLI GEL+ + GR  DVFNPSTG+A+ K+PLA RET+Q AIDAAKAAFPAWRNTP
Sbjct: 1   MSVIPHLINGELVTENGRAVDVFNPSTGQAIHKLPLATRETIQSAIDAAKAAFPAWRNTP 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 AVDALIEAPEVKALSFVGSTPIAEYIYSEGTKRG
Sbjct: 181 TLLIAQLLLEAGLPKGVLSVVHGDKTAVDALIEAPEVKALSFVGSTPIAEYIYSEGTKRG 240

Query: 241 KRVQALGGAKNHAVLMPDADLDNAVSALMGAAYGSCGERCMAISVAVCVGDQIADALVQK 300
           KRVQALGGAKNHAVLMPDADLDNAVSALMGAAYGSCGERCMAISVAVCVG+Q+ADALV K
Sbjct: 241 KRVQALGGAKNHAVLMPDADLDNAVSALMGAAYGSCGERCMAISVAVCVGEQVADALVAK 300

Query: 301 LVPQIKGLKIGAGTSCGLDMGPLVTGAARDKVTGYIDTGVAQGAELVVDGRGYKVAGHEN 360
           LVPQIK LKIGAGT+CGLDMGPLVTG ARDKV+GY++ GVA GA LVVDGRG  VAGHE 
Sbjct: 301 LVPQIKALKIGAGTNCGLDMGPLVTGQARDKVSGYVEDGVAAGATLVVDGRGLTVAGHEE 360

Query: 361 GFFLGGTLFDRVTPEMTIYKEEIFGPVLCIVRVNSLEEAMQLINDHEYGNGTCIFTRDGE 420
           GFFLGG LFD VTPEM IYKEEIFGPVLC+VRVNSLEEAMQLINDHEYGNGTCIFTRDGE
Sbjct: 361 GFFLGGCLFDNVTPEMRIYKEEIFGPVLCVVRVNSLEEAMQLINDHEYGNGTCIFTRDGE 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: 904
Number of extensions: 17
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 PfGW456L13_2 (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.5440.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-212  690.8   0.0   5.1e-212  690.6   0.0    1.0  1  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2  Methylmalonate-semialdehyde dehy


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2  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 !  690.6   0.0  5.1e-212  5.1e-212       3     477 .]       6     481 ..       4     481 .. 0.99

  Alignments for each domain:
  == domain 1  score: 690.6 bits;  conditional E-value: 5.1e-212
                                            TIGR01722   3 hlidGkfvegksdkyipvsnpatnevlakvaeasaeevdaavasaretfaawaetsva 60 
                                                          hli+G++v   +++ ++v np t++ + k++ a+ e +++a+ +a+ +f+aw++t+ a
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2   6 HLINGELVTE-NGRAVDVFNPSTGQAIHKLPLATRETIQSAIDAAKAAFPAWRNTPPA 62 
                                                          8999999965.56899****************************************** PP

                                            TIGR01722  61 erarvllryqallkehrdeiaklisaeqGktledakGdvarGlevvehacsvtslllG 118
                                                          +ra+v++r+++ll++++  ia+lis e+Gktleda G++ rG+e ve+ac+ + +l+G
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2  63 KRAQVMFRFKQLLEQNEARIAQLISEEHGKTLEDAAGELKRGIENVEFACAAPEILKG 120
                                                          ********************************************************** PP

                                            TIGR01722 119 etvesvakdvdvysirqplGvvaGitpfnfpamiplwmfplaiacGntfvlkpsekvp 176
                                                          e + +v  ++d +s  qplGvvaGitpfnfpam+plwm+plai+cGn+f+lkpse++p
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2 121 EYSRNVGPNIDAWSDFQPLGVVAGITPFNFPAMVPLWMYPLAIVCGNCFILKPSERDP 178
                                                          ********************************************************** PP

                                            TIGR01722 177 saavklaellseaGapdGvlnvvhGdkeavdrllehpdvkavsfvGsvavgeyiyetg 234
                                                          s+++ +a+ll+eaG+p+Gvl vvhGdk avd l+e p+vka+sfvGs++++eyiy+ g
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2 179 SSTLLIAQLLLEAGLPKGVLSVVHGDKTAVDALIEAPEVKALSFVGSTPIAEYIYSEG 236
                                                          ********************************************************** PP

                                            TIGR01722 235 sahgkrvqalaGaknhmvvlpdadkeaaldalvgaavGaaGqrcmaisaavlvGaa.. 290
                                                          +++gkrvqal+Gaknh+v++pdad+++a++al+gaa+G+ G+rcmais+av vG+   
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2 237 TKRGKRVQALGGAKNHAVLMPDADLDNAVSALMGAAYGSCGERCMAISVAVCVGEQva 294
                                                          ******************************************************9556 PP

                                            TIGR01722 291 kelveeireraekvrvgagddpgaelGplitkqakervasliasgakeGaevlldGrg 348
                                                          + lv +++ +++ +++gag++ g ++Gpl+t qa+++v+ ++++g++ Ga +++dGrg
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2 295 DALVAKLVPQIKALKIGAGTNCGLDMGPLVTGQARDKVSGYVEDGVAAGATLVVDGRG 352
                                                          99******************************************************** PP

                                            TIGR01722 349 ykveGyeeGnfvGitllervkpdmkiykeeifGpvlvvleadtleeaiklinespyGn 406
                                                          ++v G+eeG f+G +l+++v p+m+iykeeifGpvl+v+++++leea++lin+  yGn
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2 353 LTVAGHEEGFFLGGCLFDNVTPEMRIYKEEIFGPVLCVVRVNSLEEAMQLINDHEYGN 410
                                                          ********************************************************** PP

                                            TIGR01722 407 GtaiftsdGaaarkfqheievGqvGvnvpipvplpffsftGwkdslfGdlhiyGkqGv 464
                                                          Gt+ift+dG aar f  eievG+vGvnvp+pvp++++sf+Gwk slfGdlh+yG +Gv
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2 411 GTCIFTRDGEAARLFCDEIEVGMVGVNVPLPVPVAYHSFGGWKRSLFGDLHAYGPDGV 468
                                                          ********************************************************** PP

                                            TIGR01722 465 rfytrlktvtarw 477
                                                          rfytr k++t rw
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2 469 RFYTRRKAITQRW 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: 10.83
//
[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 (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:

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. 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:

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, 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