Alignments for a candidate for edd in Pseudomonas fluorescens FW300-N1B4

GapMind for catabolism of small carbon sources

Alignments for a candidate for edd in Pseudomonas fluorescens FW300-N1B4

Align phosphogluconate dehydratase (EC 4.2.1.12) (characterized)
to candidate Pf1N1B4_601 Phosphogluconate dehydratase (EC 4.2.1.12)

Query= BRENDA::Q1PAG1
         (608 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_601
          Length = 608

 Score = 1128 bits (2917), Expect = 0.0
 Identities = 568/607 (93%), Positives = 588/607 (96%)

Query: 1   MHPRVLEVTERLVARSRATREAYLALIRGAASDGPQRGKLQCANFAHGVAGCGSEDKHSL 60
           MHPRVLEVTERL+ARSR TREAYLALIRGAASDGP RGKLQCANFAHGVAGCGS+DKHSL
Sbjct: 1   MHPRVLEVTERLIARSRTTREAYLALIRGAASDGPMRGKLQCANFAHGVAGCGSDDKHSL 60

Query: 61  RMMNAANVAIVSSYNDMLSAHQPYEHFPEQIKKALREMGSVGQFAGGTPAMCDGVTQGEA 120
           RMMN+AN+AIVSSYNDMLSAHQPYE FPEQIKKALRE+GSVGQFAGGTPAMCDGVTQGE 
Sbjct: 61  RMMNSANIAIVSSYNDMLSAHQPYEVFPEQIKKALREIGSVGQFAGGTPAMCDGVTQGEP 120

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

Query: 181 MPSGISNKEKADVRQRYAEGKATREELLESEMKSYHSPGTCTFYGTANTNQLLMEVMGLH 240
           M SGISNK+KADVRQRYAEGKATREELLESEMKSYHSPGTCTFYGTANTNQLLMEVMGLH
Sbjct: 181 MVSGISNKQKADVRQRYAEGKATREELLESEMKSYHSPGTCTFYGTANTNQLLMEVMGLH 240

Query: 241 LPGASFVNPYTPLRDALTHEAAQQVTRLTKQSGNFTPIGEIVDERSLVNSIVALHATGGS 300
           LPGASFVNP TPLRDALT EAA QVTRLTKQSG+F PIGEIVDE SLVNSIVALHATGGS
Sbjct: 241 LPGASFVNPNTPLRDALTREAAHQVTRLTKQSGDFMPIGEIVDECSLVNSIVALHATGGS 300

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

Query: 361 LEAGLLHEDVNTVAGRGLSRYTQEPFLDNGKLVWRDGPIESLDENILRPVARAFSPEGGL 420
           LEAGLLHE+VNTV G GLSRYT EPFL+NG+LVWR+GPIESLDE ILRPVARAFSPEGGL
Sbjct: 361 LEAGLLHENVNTVLGHGLSRYTMEPFLENGELVWREGPIESLDETILRPVARAFSPEGGL 420

Query: 421 RVMEGNLGRGVMKVSAVALQHQIVEAPAVVFQDQQDLADAFKAGELEKDFVAVMRFQGPR 480
           RVMEGNLGRGVMKVSAVAL++Q+VEAPA+VFQDQQDLADAFKAG LEKDFVAVMRFQGPR
Sbjct: 421 RVMEGNLGRGVMKVSAVALENQVVEAPAMVFQDQQDLADAFKAGLLEKDFVAVMRFQGPR 480

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

Query: 541 GDIIRVDGVKGTLELKVDADEFAAREPAKGLLGNNVGSGRELFGFMRMAFSSAEQGASAF 600
           GDIIRVDGVKGTLELKVDA+EFAAREPAKGLLGNN+GSGRELFGFMRMAFSSAEQGASAF
Sbjct: 541 GDIIRVDGVKGTLELKVDAEEFAAREPAKGLLGNNIGSGRELFGFMRMAFSSAEQGASAF 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: 1361
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 Pf1N1B4_601 (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.14355.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 1023.2   0.4          0 1023.1   0.4    1.0  1  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_601  Phosphogluconate dehydratase (EC


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_601  Phosphogluconate dehydratase (EC 4.2.1.12)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1023.1   0.4         0         0       1     601 []       2     601 ..       2     601 .. 0.99

  Alignments for each domain:
  == domain 1  score: 1023.1 bits;  conditional E-value: 0
                                     TIGR01196   1 hsrlaeiteriierskktrekylekirsaktkgklrstlgcgnlahgvaalsesekvelksekrk 65 
                                                   h+r++e+ter+i+rs++tre+yl+ ir a++ g++r++l c+n+ahgva +  ++k +l+ ++ +
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_601   2 HPRVLEVTERLIARSRTTREAYLALIRGAASDGPMRGKLQCANFAHGVAGCGSDDKHSLRMMNSA 66 
                                                   79*************************************************************** PP

                                     TIGR01196  66 nlaiitayndmlsahqpfkeypdlikkalqeanavaqvagGvpamcdGvtqGedGmelsllsrdv 130
                                                   n+ai+++yndmlsahqp++ +p++ikkal+e ++v+q agG+pamcdGvtqGe+Gmelsl sr+v
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_601  67 NIAIVSSYNDMLSAHQPYEVFPEQIKKALREIGSVGQFAGGTPAMCDGVTQGEPGMELSLPSREV 131
                                                   ***************************************************************** PP

                                     TIGR01196 131 ialstaiglshnmfdgalflGvcdkivpGlliaalsfGhlpavfvpaGpmasGlenkekakvrql 195
                                                   ialsta++lshnmfdgal+lG+cdkivpGl+++al fGhlp++fvp+Gpm+sG++nk+ka vrq 
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_601 132 IALSTAVALSHNMFDGALMLGICDKIVPGLMMGALRFGHLPTIFVPGGPMVSGISNKQKADVRQR 196
                                                   ***************************************************************** PP

                                     TIGR01196 196 faeGkvdreellksemasyhapGtctfyGtansnqmlvelmGlhlpgasfvnpntplrdaltrea 260
                                                   +aeGk++reell+sem+syh+pGtctfyGtan+nq+l+e+mGlhlpgasfvnpntplrdaltrea
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_601 197 YAEGKATREELLESEMKSYHSPGTCTFYGTANTNQLLMEVMGLHLPGASFVNPNTPLRDALTREA 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__pseudo1_N1B4:Pf1N1B4_601 262 AHQVTRLTKQSGDFMPIGEIVDECSLVNSIVALHATGGSTNHTLHMPAIAMAAGIQLTWQDMADL 326
                                                   ***************************************************************** PP

                                     TIGR01196 326 sdlvpllarvypnGkadvnhfeaaGGlsflirellkeGllhedvetvagkGlrrytkepfledgk 390
                                                   s++vp+l +vypnGkad+nhf+aaGG+sflirell++Gllhe+v+tv+g+Gl+ryt+epfle+g+
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_601 327 SEVVPTLSHVYPNGKADINHFQAAGGMSFLIRELLEAGLLHENVNTVLGHGLSRYTMEPFLENGE 391
                                                   ***************************************************************** PP

                                     TIGR01196 391 leyreaaeksldedilrkvdkpfsaeGGlkllkGnlGravikvsavkeesrvieapaivfkdqae 455
                                                   l++re++ +slde ilr+v + fs+eGGl++++GnlGr+v+kvsav+ e++v+eapa+vf+dq++
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_601 392 LVWREGPIESLDETILRPVARAFSPEGGLRVMEGNLGRGVMKVSAVALENQVVEAPAMVFQDQQD 456
                                                   ***************************************************************** PP

                                     TIGR01196 456 llaafkagelerdlvavvrfqGpkanGmpelhklttvlGvlqdrgfkvalvtdGrlsGasGkvpa 520
                                                   l++afkag le+d+vav+rfqGp++nGmpelhk+t++lGvlqdrgfkvalvtdGr+sGasGk+pa
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_601 457 LADAFKAGLLEKDFVAVMRFQGPRSNGMPELHKMTPFLGVLQDRGFKVALVTDGRMSGASGKIPA 521
                                                   ***************************************************************** PP

                                     TIGR01196 521 aihvtpealegGalakirdGdlirldavngelevlvddaelkareleeldlednelGlGrelfaa 585
                                                   aihv+pea+ gGala++++Gd+ir+d+v+g le+ vd  e++are+++  l  n++G Grelf +
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_601 522 AIHVSPEAYVGGALARVQEGDIIRVDGVKGTLELKVDAEEFAAREPAK-GLLGNNIGSGRELFGF 585
                                                   *********************************************876.566789********** PP

                                     TIGR01196 586 lrekvssaeeGasslt 601
                                                   +r + ssae+Gas++t
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_601 586 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: 7.75
//
[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)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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