GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1889
          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.2229777.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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 18.27
//
[ok]

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

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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:

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