GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__pseudo5_N2C3_1:AO356_05220
          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.833966.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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 27.83
//
[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 (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