GapMind for catabolism of small carbon sources

 

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

Align phosphogluconate dehydratase (EC 4.2.1.12) (characterized)
to candidate PfGW456L13_1889 Phosphogluconate dehydratase (EC 4.2.1.12)

Query= BRENDA::Q1PAG1
         (608 letters)



>lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1889
           Phosphogluconate dehydratase (EC 4.2.1.12)
          Length = 608

 Score = 1114 bits (2881), Expect = 0.0
 Identities = 561/607 (92%), Positives = 586/607 (96%)

Query: 1   MHPRVLEVTERLVARSRATREAYLALIRGAASDGPQRGKLQCANFAHGVAGCGSEDKHSL 60
           MHPRVLEVTERL+ARSRATREAYLALIRGAASDGP RGKLQCANFAHGVAGCGS+DKHSL
Sbjct: 1   MHPRVLEVTERLIARSRATREAYLALIRGAASDGPMRGKLQCANFAHGVAGCGSDDKHSL 60

Query: 61  RMMNAANVAIVSSYNDMLSAHQPYEHFPEQIKKALREMGSVGQFAGGTPAMCDGVTQGEA 120
           RMMN+AN+AIVSSYNDMLSAHQPYE FPE IKKALRE+GSVGQFAGGTPAMCDGVTQGE 
Sbjct: 61  RMMNSANIAIVSSYNDMLSAHQPYEVFPELIKKALREIGSVGQFAGGTPAMCDGVTQGEP 120

Query: 121 GMELSLPSREVIALSTAVALSHNMFDAALMLGICDKIVPGLMMGALRFGHLPTIFVPGGP 180
           GMELSLPSREVIALSTAVALSHNMFD AL+LGICDKIVPGLMMGALRFGHLP IFVPGGP
Sbjct: 121 GMELSLPSREVIALSTAVALSHNMFDGALLLGICDKIVPGLMMGALRFGHLPMIFVPGGP 180

Query: 181 MPSGISNKEKADVRQRYAEGKATREELLESEMKSYHSPGTCTFYGTANTNQLLMEVMGLH 240
           M SGISNK+KADVRQ+YAEGKATREELLESEMKSYHSPGTCTFYGTANTNQLLMEVMGLH
Sbjct: 181 MVSGISNKQKADVRQKYAEGKATREELLESEMKSYHSPGTCTFYGTANTNQLLMEVMGLH 240

Query: 241 LPGASFVNPYTPLRDALTHEAAQQVTRLTKQSGNFTPIGEIVDERSLVNSIVALHATGGS 300
           LPGASFVNP TPLRDALT EAA QVTRLTKQ+G+F PIGEIVDERSLVNSIVALHATGGS
Sbjct: 241 LPGASFVNPNTPLRDALTREAAHQVTRLTKQNGDFMPIGEIVDERSLVNSIVALHATGGS 300

Query: 301 TNHTLHMPAIAQAAGIQLTWQDMADLSEVVPTLSHVYPNGKADINHFQAAGGMAFLIREL 360
           TNHTLHMPAIA AAGIQLTWQDMADLSEVVPTLSHVYPNGKADINHFQAAGGM+FLIREL
Sbjct: 301 TNHTLHMPAIAMAAGIQLTWQDMADLSEVVPTLSHVYPNGKADINHFQAAGGMSFLIREL 360

Query: 361 LEAGLLHEDVNTVAGRGLSRYTQEPFLDNGKLVWRDGPIESLDENILRPVARAFSPEGGL 420
           LEAGLLHE+VNTV G GLSRYTQEPFLDNG+LVWR+G  +SLDE+ILRPVARAFS EGGL
Sbjct: 361 LEAGLLHENVNTVMGHGLSRYTQEPFLDNGQLVWREGVTDSLDESILRPVARAFSAEGGL 420

Query: 421 RVMEGNLGRGVMKVSAVALQHQIVEAPAVVFQDQQDLADAFKAGELEKDFVAVMRFQGPR 480
           RVMEGNLGRGVMKVSAVA+++QIVEAPA+VFQDQQDLADAFKAG LEKDFVAVMRFQGPR
Sbjct: 421 RVMEGNLGRGVMKVSAVAVENQIVEAPAMVFQDQQDLADAFKAGLLEKDFVAVMRFQGPR 480

Query: 481 SNGMPELHKMTPFLGVLQDRGFKVALVTDGRMSGASGKIPAAIHVSPEAQVGGALARVRD 540
           SNGMPELHKMTPFLGVLQDRGFKVALVTDGRMSGASGKIPAAIHVSPEA VGGALARV++
Sbjct: 481 SNGMPELHKMTPFLGVLQDRGFKVALVTDGRMSGASGKIPAAIHVSPEAYVGGALARVQE 540

Query: 541 GDIIRVDGVKGTLELKVDADEFAAREPAKGLLGNNVGSGRELFGFMRMAFSSAEQGASAF 600
           GDIIRVDGVKGTLELKVDA+EFAAR PAKGLLGNN+G+GRELFGFMRMAFSSAEQGASAF
Sbjct: 541 GDIIRVDGVKGTLELKVDAEEFAARTPAKGLLGNNIGTGRELFGFMRMAFSSAEQGASAF 600

Query: 601 TSALENL 607
           TSALE L
Sbjct: 601 TSALETL 607


Lambda     K      H
   0.318    0.134    0.386 

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: 1341
Number of extensions: 44
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: 608
Length of database: 608
Length adjustment: 37
Effective length of query: 571
Effective length of database: 571
Effective search space:   326041
Effective search space used:   326041
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: 53 (25.0 bits)

Align candidate PfGW456L13_1889 (Phosphogluconate dehydratase (EC 4.2.1.12))
to HMM TIGR01196 (edd: phosphogluconate dehydratase (EC 4.2.1.12))

# 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/TIGR01196.hmm
# target sequence database:        /tmp/gapView.15297.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01196  [M=601]
Accession:   TIGR01196
Description: edd: phosphogluconate dehydratase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                               -----------
          0 1029.7   1.1          0 1029.5   1.1    1.0  1  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1889  Phosphogluconate dehydratase (EC


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1889  Phosphogluconate dehydratase (EC 4.2.1.12)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1029.5   1.1         0         0       1     601 []       2     601 ..       2     601 .. 0.99

  Alignments for each domain:
  == domain 1  score: 1029.5 bits;  conditional E-value: 0
                                               TIGR01196   1 hsrlaeiteriierskktrekylekirsaktkgklrstlgcgnlahgvaalsese 55 
                                                             h+r++e+ter+i+rs++tre+yl+ ir a++ g++r++l c+n+ahgva +  ++
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1889   2 HPRVLEVTERLIARSRATREAYLALIRGAASDGPMRGKLQCANFAHGVAGCGSDD 56 
                                                             79***************************************************** PP

                                               TIGR01196  56 kvelksekrknlaiitayndmlsahqpfkeypdlikkalqeanavaqvagGvpam 110
                                                             k +l+ ++ +n+ai+++yndmlsahqp++ +p+likkal+e ++v+q agG+pam
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1889  57 KHSLRMMNSANIAIVSSYNDMLSAHQPYEVFPELIKKALREIGSVGQFAGGTPAM 111
                                                             ******************************************************* PP

                                               TIGR01196 111 cdGvtqGedGmelsllsrdvialstaiglshnmfdgalflGvcdkivpGlliaal 165
                                                             cdGvtqGe+Gmelsl sr+vialsta++lshnmfdgal+lG+cdkivpGl+++al
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1889 112 CDGVTQGEPGMELSLPSREVIALSTAVALSHNMFDGALLLGICDKIVPGLMMGAL 166
                                                             ******************************************************* PP

                                               TIGR01196 166 sfGhlpavfvpaGpmasGlenkekakvrqlfaeGkvdreellksemasyhapGtc 220
                                                              fGhlp +fvp+Gpm+sG++nk+ka vrq +aeGk++reell+sem+syh+pGtc
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1889 167 RFGHLPMIFVPGGPMVSGISNKQKADVRQKYAEGKATREELLESEMKSYHSPGTC 221
                                                             ******************************************************* PP

                                               TIGR01196 221 tfyGtansnqmlvelmGlhlpgasfvnpntplrdaltreaakrlarltakngevl 275
                                                             tfyGtan+nq+l+e+mGlhlpgasfvnpntplrdaltreaa++++rlt +ng+++
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1889 222 TFYGTANTNQLLMEVMGLHLPGASFVNPNTPLRDALTREAAHQVTRLTKQNGDFM 276
                                                             ******************************************************* PP

                                               TIGR01196 276 plaelideksivnalvgllatGGstnhtlhlvaiaraaGiilnwddlselsdlvp 330
                                                             p++e++de+s+vn++v+l+atGGstnhtlh+ aia aaGi+l+w+d+ +ls++vp
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1889 277 PIGEIVDERSLVNSIVALHATGGSTNHTLHMPAIAMAAGIQLTWQDMADLSEVVP 331
                                                             ******************************************************* PP

                                               TIGR01196 331 llarvypnGkadvnhfeaaGGlsflirellkeGllhedvetvagkGlrrytkepf 385
                                                             +l +vypnGkad+nhf+aaGG+sflirell++Gllhe+v+tv+g+Gl+ryt+epf
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1889 332 TLSHVYPNGKADINHFQAAGGMSFLIRELLEAGLLHENVNTVMGHGLSRYTQEPF 386
                                                             ******************************************************* PP

                                               TIGR01196 386 ledgkleyreaaeksldedilrkvdkpfsaeGGlkllkGnlGravikvsavkees 440
                                                             l++g+l++re++  slde+ilr+v + fsaeGGl++++GnlGr+v+kvsav+ e+
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1889 387 LDNGQLVWREGVTDSLDESILRPVARAFSAEGGLRVMEGNLGRGVMKVSAVAVEN 441
                                                             ******************************************************* PP

                                               TIGR01196 441 rvieapaivfkdqaellaafkagelerdlvavvrfqGpkanGmpelhklttvlGv 495
                                                             +++eapa+vf+dq++l++afkag le+d+vav+rfqGp++nGmpelhk+t++lGv
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1889 442 QIVEAPAMVFQDQQDLADAFKAGLLEKDFVAVMRFQGPRSNGMPELHKMTPFLGV 496
                                                             ******************************************************* PP

                                               TIGR01196 496 lqdrgfkvalvtdGrlsGasGkvpaaihvtpealegGalakirdGdlirldavng 550
                                                             lqdrgfkvalvtdGr+sGasGk+paaihv+pea+ gGala++++Gd+ir+d+v+g
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1889 497 LQDRGFKVALVTDGRMSGASGKIPAAIHVSPEAYVGGALARVQEGDIIRVDGVKG 551
                                                             ******************************************************* PP

                                               TIGR01196 551 elevlvddaelkareleeldlednelGlGrelfaalrekvssaeeGasslt 601
                                                              le+ vd  e++ar++++  l  n++G+Grelf ++r + ssae+Gas++t
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1889 552 TLELKVDAEEFAARTPAK-GLLGNNIGTGRELFGFMRMAFSSAEQGASAFT 601
                                                             ***************776.566789**********************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (601 nodes)
Target sequences:                          1  (608 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: 12.76
//
[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