Alignments for a candidate for edd in Pseudomonas fluorescens FW300-N2E3

GapMind for catabolism of small carbon sources

Alignments for a candidate for edd in Pseudomonas fluorescens FW300-N2E3

Align phosphogluconate dehydratase (EC 4.2.1.12) (characterized)
to candidate AO353_03420 AO353_03420 phosphogluconate dehydratase

Query= BRENDA::Q1PAG1
         (608 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_03420
          Length = 608

 Score = 1122 bits (2902), Expect = 0.0
 Identities = 565/608 (92%), Positives = 584/608 (96%)

Query: 1   MHPRVLEVTERLVARSRATREAYLALIRGAASDGPQRGKLQCANFAHGVAGCGSEDKHSL 60
           MHPRVLEVTERLV RSRATREAYLALIRGAASDGP RGKLQCANFAHGVAGCG+EDK SL
Sbjct: 1   MHPRVLEVTERLVTRSRATREAYLALIRGAASDGPMRGKLQCANFAHGVAGCGTEDKQSL 60

Query: 61  RMMNAANVAIVSSYNDMLSAHQPYEHFPEQIKKALREMGSVGQFAGGTPAMCDGVTQGEA 120
           RMMNAANVAIVSSYNDMLSAHQPYEH+PEQIK ALRE+GSVGQFAGG PAMCDGVTQGE 
Sbjct: 61  RMMNAANVAIVSSYNDMLSAHQPYEHYPEQIKHALREIGSVGQFAGGVPAMCDGVTQGEP 120

Query: 121 GMELSLPSREVIALSTAVALSHNMFDAALMLGICDKIVPGLMMGALRFGHLPTIFVPGGP 180
           GMEL + SREVIA+STAVALSHNMFDAA+MLGICDKIVPGLMMGALRFGHLPTIFVPGGP
Sbjct: 121 GMELGIASREVIAMSTAVALSHNMFDAAMMLGICDKIVPGLMMGALRFGHLPTIFVPGGP 180

Query: 181 MPSGISNKEKADVRQRYAEGKATREELLESEMKSYHSPGTCTFYGTANTNQLLMEVMGLH 240
           M SGISNKEKADVRQRYAEGKA+REELLESEMKSYHSPGTCTFYGTANTNQLLMEVMGLH
Sbjct: 181 MVSGISNKEKADVRQRYAEGKASREELLESEMKSYHSPGTCTFYGTANTNQLLMEVMGLH 240

Query: 241 LPGASFVNPYTPLRDALTHEAAQQVTRLTKQSGNFTPIGEIVDERSLVNSIVALHATGGS 300
           LPGASFVNP TPLRDALT EAA Q+TRLTKQSGNF PIGEIVDERSLVNSIVALHATGGS
Sbjct: 241 LPGASFVNPNTPLRDALTREAAHQITRLTKQSGNFMPIGEIVDERSLVNSIVALHATGGS 300

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

Query: 361 LEAGLLHEDVNTVAGRGLSRYTQEPFLDNGKLVWRDGPIESLDENILRPVARAFSPEGGL 420
           LEAGLLHEDVNTVAG GLSRYTQEPFL+NG+LVWR+GPIESLDENILRPVARAFSPEGGL
Sbjct: 361 LEAGLLHEDVNTVAGHGLSRYTQEPFLENGELVWREGPIESLDENILRPVARAFSPEGGL 420

Query: 421 RVMEGNLGRGVMKVSAVALQHQIVEAPAVVFQDQQDLADAFKAGELEKDFVAVMRFQGPR 480
           RVMEGNLGRGVMKVSAVA +HQ+VEAPA+VFQDQQDLADAFKAG LEKDFVAVMRFQGPR
Sbjct: 421 RVMEGNLGRGVMKVSAVAPEHQVVEAPAMVFQDQQDLADAFKAGLLEKDFVAVMRFQGPR 480

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

Query: 541 GDIIRVDGVKGTLELKVDADEFAAREPAKGLLGNNVGSGRELFGFMRMAFSSAEQGASAF 600
           GDIIRVDGVKGTL+L VDADEFAAR PAKGLL N +G GRELFGFMRMAFSSAEQGASAF
Sbjct: 541 GDIIRVDGVKGTLQLLVDADEFAARTPAKGLLDNGIGCGRELFGFMRMAFSSAEQGASAF 600

Query: 601 TSALENLK 608
           TSALE LK
Sbjct: 601 TSALETLK 608


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: 1351
Number of extensions: 49
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 AO353_03420 AO353_03420 (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.31585.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 1040.1   0.8          0 1039.9   0.8    1.0  1  lcl|FitnessBrowser__pseudo3_N2E3:AO353_03420  AO353_03420 phosphogluconate deh


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo3_N2E3:AO353_03420  AO353_03420 phosphogluconate dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1039.9   0.8         0         0       1     601 []       2     601 ..       2     601 .. 0.99

  Alignments for each domain:
  == domain 1  score: 1039.9 bits;  conditional E-value: 0
                                     TIGR01196   1 hsrlaeiteriierskktrekylekirsaktkgklrstlgcgnlahgvaalsesekvelksekrk 65 
                                                   h+r++e+ter++ rs++tre+yl+ ir a++ g++r++l c+n+ahgva +  ++k++l+ ++ +
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_03420   2 HPRVLEVTERLVTRSRATREAYLALIRGAASDGPMRGKLQCANFAHGVAGCGTEDKQSLRMMNAA 66 
                                                   79*************************************************************** PP

                                     TIGR01196  66 nlaiitayndmlsahqpfkeypdlikkalqeanavaqvagGvpamcdGvtqGedGmelsllsrdv 130
                                                   n+ai+++yndmlsahqp+++yp++ik+al+e ++v+q agGvpamcdGvtqGe+Gmel ++sr+v
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_03420  67 NVAIVSSYNDMLSAHQPYEHYPEQIKHALREIGSVGQFAGGVPAMCDGVTQGEPGMELGIASREV 131
                                                   ***************************************************************** PP

                                     TIGR01196 131 ialstaiglshnmfdgalflGvcdkivpGlliaalsfGhlpavfvpaGpmasGlenkekakvrql 195
                                                   ia+sta++lshnmfd+a++lG+cdkivpGl+++al fGhlp++fvp+Gpm+sG++nkeka vrq 
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_03420 132 IAMSTAVALSHNMFDAAMMLGICDKIVPGLMMGALRFGHLPTIFVPGGPMVSGISNKEKADVRQR 196
                                                   ***************************************************************** PP

                                     TIGR01196 196 faeGkvdreellksemasyhapGtctfyGtansnqmlvelmGlhlpgasfvnpntplrdaltrea 260
                                                   +aeGk++reell+sem+syh+pGtctfyGtan+nq+l+e+mGlhlpgasfvnpntplrdaltrea
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_03420 197 YAEGKASREELLESEMKSYHSPGTCTFYGTANTNQLLMEVMGLHLPGASFVNPNTPLRDALTREA 261
                                                   ***************************************************************** PP

                                     TIGR01196 261 akrlarltakngevlplaelideksivnalvgllatGGstnhtlhlvaiaraaGiilnwddlsel 325
                                                   a++++rlt ++g+++p++e++de+s+vn++v+l+atGGstnhtlh+ aia aaGi+l+w+d+ +l
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_03420 262 AHQITRLTKQSGNFMPIGEIVDERSLVNSIVALHATGGSTNHTLHMPAIAMAAGIQLTWQDMADL 326
                                                   ***************************************************************** PP

                                     TIGR01196 326 sdlvpllarvypnGkadvnhfeaaGGlsflirellkeGllhedvetvagkGlrrytkepfledgk 390
                                                   s++vp+l +vypnGkad+nhf+aaGG+sflirell++Gllhedv+tvag+Gl+ryt+epfle+g+
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_03420 327 SEVVPTLSHVYPNGKADINHFQAAGGMSFLIRELLEAGLLHEDVNTVAGHGLSRYTQEPFLENGE 391
                                                   ***************************************************************** PP

                                     TIGR01196 391 leyreaaeksldedilrkvdkpfsaeGGlkllkGnlGravikvsavkeesrvieapaivfkdqae 455
                                                   l++re++ +slde+ilr+v + fs+eGGl++++GnlGr+v+kvsav++e++v+eapa+vf+dq++
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_03420 392 LVWREGPIESLDENILRPVARAFSPEGGLRVMEGNLGRGVMKVSAVAPEHQVVEAPAMVFQDQQD 456
                                                   ***************************************************************** PP

                                     TIGR01196 456 llaafkagelerdlvavvrfqGpkanGmpelhklttvlGvlqdrgfkvalvtdGrlsGasGkvpa 520
                                                   l++afkag le+d+vav+rfqGp++nGmpelhk+t++lGvlqdrgfkvalvtdGr+sGasGk+pa
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_03420 457 LADAFKAGLLEKDFVAVMRFQGPRSNGMPELHKMTPFLGVLQDRGFKVALVTDGRMSGASGKIPA 521
                                                   ***************************************************************** PP

                                     TIGR01196 521 aihvtpealegGalakirdGdlirldavngelevlvddaelkareleeldlednelGlGrelfaa 585
                                                   aihv+pea  gGala++++Gd+ir+d+v+g l++lvd  e++ar++++  l dn +G+Grelf +
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_03420 522 AIHVSPEAFVGGALARVQEGDIIRVDGVKGTLQLLVDADEFAARTPAK-GLLDNGIGCGRELFGF 585
                                                   *********************************************765.688999********** PP

                                     TIGR01196 586 lrekvssaeeGasslt 601
                                                   +r + ssae+Gas++t
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_03420 586 MRMAFSSAEQGASAFT 601
                                                   ************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: 9.04
//
[ok]

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

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Candidates (tab-delimited)
Steps (tab-delimited)
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Protein sequences (fasta format)
Organisms (tab-delimited)
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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources