GapMind for catabolism of small carbon sources

 

Aligments for a candidate for edd in Pseudomonas fluorescens FW300-N2C3

Align phosphogluconate dehydratase (EC 4.2.1.12) (characterized)
to candidate AO356_05220 AO356_05220 phosphogluconate dehydratase

Query= BRENDA::Q1PAG1
         (608 letters)



>lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_05220 AO356_05220
           phosphogluconate dehydratase
          Length = 608

 Score = 1132 bits (2928), Expect = 0.0
 Identities = 571/607 (94%), Positives = 590/607 (97%)

Query: 1   MHPRVLEVTERLVARSRATREAYLALIRGAASDGPQRGKLQCANFAHGVAGCGSEDKHSL 60
           MHPRVLEVTERL+ARSRATR+AYLALIR AASDGP RGKLQCANFAHGVAGCG+EDKH L
Sbjct: 1   MHPRVLEVTERLIARSRATRQAYLALIRDAASDGPMRGKLQCANFAHGVAGCGTEDKHHL 60

Query: 61  RMMNAANVAIVSSYNDMLSAHQPYEHFPEQIKKALREMGSVGQFAGGTPAMCDGVTQGEA 120
           RMMNAAN+AIVSSYNDMLSAHQPYE FPEQIKKALRE+GSVGQFAGGTPAMCDGVTQGEA
Sbjct: 61  RMMNAANIAIVSSYNDMLSAHQPYETFPEQIKKALREIGSVGQFAGGTPAMCDGVTQGEA 120

Query: 121 GMELSLPSREVIALSTAVALSHNMFDAALMLGICDKIVPGLMMGALRFGHLPTIFVPGGP 180
           GMELSLPSREVIALSTAVALSHNMFD ALMLGICDKIVPGLMMGALRFGHLPTIFVPGGP
Sbjct: 121 GMELSLPSREVIALSTAVALSHNMFDGALMLGICDKIVPGLMMGALRFGHLPTIFVPGGP 180

Query: 181 MPSGISNKEKADVRQRYAEGKATREELLESEMKSYHSPGTCTFYGTANTNQLLMEVMGLH 240
           M SGISNKEKADVRQRYAEGKATREELLESEMKSYHSPGTCTFYGTANTNQLLMEVMGLH
Sbjct: 181 MVSGISNKEKADVRQRYAEGKATREELLESEMKSYHSPGTCTFYGTANTNQLLMEVMGLH 240

Query: 241 LPGASFVNPYTPLRDALTHEAAQQVTRLTKQSGNFTPIGEIVDERSLVNSIVALHATGGS 300
           LPGASFVNP TPLRDALT EAA QVTR+TKQSGNF PIGEIVDERSLVNSIVALHATGGS
Sbjct: 241 LPGASFVNPNTPLRDALTREAAFQVTRMTKQSGNFMPIGEIVDERSLVNSIVALHATGGS 300

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

Query: 361 LEAGLLHEDVNTVAGRGLSRYTQEPFLDNGKLVWRDGPIESLDENILRPVARAFSPEGGL 420
           LEAGLLHE+VNTV G GLSRYTQEPFL++G+LVWRDGPIESLDENILRPVARAFSPEGGL
Sbjct: 361 LEAGLLHENVNTVLGHGLSRYTQEPFLEDGELVWRDGPIESLDENILRPVARAFSPEGGL 420

Query: 421 RVMEGNLGRGVMKVSAVALQHQIVEAPAVVFQDQQDLADAFKAGELEKDFVAVMRFQGPR 480
           RVMEGNLGRGVMKVSAVAL++QIVEAPA+VFQDQQDLADAFKAG LEKDFVAVMRFQGPR
Sbjct: 421 RVMEGNLGRGVMKVSAVALENQIVEAPAMVFQDQQDLADAFKAGLLEKDFVAVMRFQGPR 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: 1375
Number of extensions: 48
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 AO356_05220 AO356_05220 (phosphogluconate dehydratase)
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.14412.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 1029.9   0.6          0 1029.7   0.6    1.0  1  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_05220  AO356_05220 phosphogluconate deh


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_05220  AO356_05220 phosphogluconate dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1029.7   0.6         0         0       1     601 []       2     601 ..       2     601 .. 0.99

  Alignments for each domain:
  == domain 1  score: 1029.7 bits;  conditional E-value: 0
                                       TIGR01196   1 hsrlaeiteriierskktrekylekirsaktkgklrstlgcgnlahgvaalsesekvelksek 63 
                                                     h+r++e+ter+i+rs++tr++yl+ ir+a++ g++r++l c+n+ahgva +  ++k +l+ ++
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_05220   2 HPRVLEVTERLIARSRATRQAYLALIRDAASDGPMRGKLQCANFAHGVAGCGTEDKHHLRMMN 64 
                                                     79************************************************************* PP

                                       TIGR01196  64 rknlaiitayndmlsahqpfkeypdlikkalqeanavaqvagGvpamcdGvtqGedGmelsll 126
                                                      +n+ai+++yndmlsahqp++++p++ikkal+e ++v+q agG+pamcdGvtqGe+Gmelsl 
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_05220  65 AANIAIVSSYNDMLSAHQPYETFPEQIKKALREIGSVGQFAGGTPAMCDGVTQGEAGMELSLP 127
                                                     *************************************************************** PP

                                       TIGR01196 127 srdvialstaiglshnmfdgalflGvcdkivpGlliaalsfGhlpavfvpaGpmasGlenkek 189
                                                     sr+vialsta++lshnmfdgal+lG+cdkivpGl+++al fGhlp++fvp+Gpm+sG++nkek
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_05220 128 SREVIALSTAVALSHNMFDGALMLGICDKIVPGLMMGALRFGHLPTIFVPGGPMVSGISNKEK 190
                                                     *************************************************************** PP

                                       TIGR01196 190 akvrqlfaeGkvdreellksemasyhapGtctfyGtansnqmlvelmGlhlpgasfvnpntpl 252
                                                     a vrq +aeGk++reell+sem+syh+pGtctfyGtan+nq+l+e+mGlhlpgasfvnpntpl
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_05220 191 ADVRQRYAEGKATREELLESEMKSYHSPGTCTFYGTANTNQLLMEVMGLHLPGASFVNPNTPL 253
                                                     *************************************************************** PP

                                       TIGR01196 253 rdaltreaakrlarltakngevlplaelideksivnalvgllatGGstnhtlhlvaiaraaGi 315
                                                     rdaltreaa +++r+t ++g+++p++e++de+s+vn++v+l+atGGstnhtlh+ aia aaGi
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_05220 254 RDALTREAAFQVTRMTKQSGNFMPIGEIVDERSLVNSIVALHATGGSTNHTLHMPAIAMAAGI 316
                                                     *************************************************************** PP

                                       TIGR01196 316 ilnwddlselsdlvpllarvypnGkadvnhfeaaGGlsflirellkeGllhedvetvagkGlr 378
                                                     +l+w+d+ +ls++vp+l +vypnGkad+nhf+aaGG+sflirell++Gllhe+v+tv+g+Gl+
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_05220 317 QLTWQDMADLSEVVPTLSHVYPNGKADINHFQAAGGMSFLIRELLEAGLLHENVNTVLGHGLS 379
                                                     *************************************************************** PP

                                       TIGR01196 379 rytkepfledgkleyreaaeksldedilrkvdkpfsaeGGlkllkGnlGravikvsavkeesr 441
                                                     ryt+epfledg+l++r+++ +slde+ilr+v + fs+eGGl++++GnlGr+v+kvsav+ e++
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_05220 380 RYTQEPFLEDGELVWRDGPIESLDENILRPVARAFSPEGGLRVMEGNLGRGVMKVSAVALENQ 442
                                                     *************************************************************** PP

                                       TIGR01196 442 vieapaivfkdqaellaafkagelerdlvavvrfqGpkanGmpelhklttvlGvlqdrgfkva 504
                                                     ++eapa+vf+dq++l++afkag le+d+vav+rfqGp++nGmpelhk+t++lGvlqdrgfkva
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_05220 443 IVEAPAMVFQDQQDLADAFKAGLLEKDFVAVMRFQGPRSNGMPELHKMTPFLGVLQDRGFKVA 505
                                                     *************************************************************** PP

                                       TIGR01196 505 lvtdGrlsGasGkvpaaihvtpealegGalakirdGdlirldavngelevlvddaelkarele 567
                                                     lvtdGr+sGasGk+paaihv+pea+ gGala++++Gd+ir+d+v+g le+ vd  e++ar+++
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_05220 506 LVTDGRMSGASGKIPAAIHVSPEAYVGGALARVQEGDIIRVDGVKGTLELKVDAEEFAARTPA 568
                                                     *************************************************************77 PP

                                       TIGR01196 568 eldlednelGlGrelfaalrekvssaeeGasslt 601
                                                     +  l  n++G+Grelf ++r + ssae+Gas++t
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_05220 569 K-GLLGNNIGTGRELFGFMRMAFSSAEQGASAFT 601
                                                     6.566789**********************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: 0.03u 0.02s 00:00:00.05 Elapsed: 00:00:00.04
# Mc/sec: 7.34
//
[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 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