Alignments for a candidate for edd in Pseudomonas simiae WCS417

GapMind for catabolism of small carbon sources

Alignments for a candidate for edd in Pseudomonas simiae WCS417

Align phosphogluconate dehydratase (EC 4.2.1.12) (characterized)
to candidate GFF4432 PS417_22690 phosphogluconate dehydratase

Query= BRENDA::Q1PAG1
         (608 letters)



>FitnessBrowser__WCS417:GFF4432
          Length = 608

 Score = 1115 bits (2883), Expect = 0.0
 Identities = 560/608 (92%), Positives = 586/608 (96%)

Query: 1   MHPRVLEVTERLVARSRATREAYLALIRGAASDGPQRGKLQCANFAHGVAGCGSEDKHSL 60
           MHPRVLEVTERL+ARSRATREAYLALIRGAA DGP RGKLQCANFAHGVAGCG+EDK+SL
Sbjct: 1   MHPRVLEVTERLIARSRATREAYLALIRGAAIDGPMRGKLQCANFAHGVAGCGTEDKNSL 60

Query: 61  RMMNAANVAIVSSYNDMLSAHQPYEHFPEQIKKALREMGSVGQFAGGTPAMCDGVTQGEA 120
           RMMNAANVAIVSSYNDMLSAHQPYEHFPEQIKKALRE+GSVGQFAGGTPAMCDGVTQGE 
Sbjct: 61  RMMNAANVAIVSSYNDMLSAHQPYEHFPEQIKKALREVGSVGQFAGGTPAMCDGVTQGEP 120

Query: 121 GMELSLPSREVIALSTAVALSHNMFDAALMLGICDKIVPGLMMGALRFGHLPTIFVPGGP 180
           GMELSL SREVIA+STAVALSHNMFDAALMLGICDKIVPGLMMGALR+GHLP IFVPGGP
Sbjct: 121 GMELSLLSREVIAMSTAVALSHNMFDAALMLGICDKIVPGLMMGALRYGHLPMIFVPGGP 180

Query: 181 MPSGISNKEKADVRQRYAEGKATREELLESEMKSYHSPGTCTFYGTANTNQLLMEVMGLH 240
           MPSGISNK+KADVRQRYAEGKATREELLESEMKSYHSPGTCTFYGTANTNQLLMEVMGLH
Sbjct: 181 MPSGISNKQKADVRQRYAEGKATREELLESEMKSYHSPGTCTFYGTANTNQLLMEVMGLH 240

Query: 241 LPGASFVNPYTPLRDALTHEAAQQVTRLTKQSGNFTPIGEIVDERSLVNSIVALHATGGS 300
           LPGASFVNPYTPLRDALT EAA QVTRLTK +G+F PIGEIVDE+S+VNSI+AL+ATGGS
Sbjct: 241 LPGASFVNPYTPLRDALTREAAHQVTRLTKANGSFMPIGEIVDEKSIVNSIIALNATGGS 300

Query: 301 TNHTLHMPAIAQAAGIQLTWQDMADLSEVVPTLSHVYPNGKADINHFQAAGGMAFLIREL 360
           TNHTLHMPAIA +AGI LTW DMADLSEVVPTLSHVYPNGKADINHFQAAGGM+FLIREL
Sbjct: 301 TNHTLHMPAIAMSAGIILTWDDMADLSEVVPTLSHVYPNGKADINHFQAAGGMSFLIREL 360

Query: 361 LEAGLLHEDVNTVAGRGLSRYTQEPFLDNGKLVWRDGPIESLDENILRPVARAFSPEGGL 420
           LEAGLLHEDVNTVAG+GLSRYTQEPFL +G+L+WR+GPIESLDE ILRPVARAFSPEGGL
Sbjct: 361 LEAGLLHEDVNTVAGKGLSRYTQEPFLVDGELIWREGPIESLDETILRPVARAFSPEGGL 420

Query: 421 RVMEGNLGRGVMKVSAVALQHQIVEAPAVVFQDQQDLADAFKAGELEKDFVAVMRFQGPR 480
           RVMEGNLGRGVMKVSAVA +HQIVEAPAVVFQDQQDLADAFKAG+LEKDFVAVMRFQGPR
Sbjct: 421 RVMEGNLGRGVMKVSAVAPEHQIVEAPAVVFQDQQDLADAFKAGQLEKDFVAVMRFQGPR 480

Query: 481 SNGMPELHKMTPFLGVLQDRGFKVALVTDGRMSGASGKIPAAIHVSPEAQVGGALARVRD 540
           SNGMPELHKMTPFLGVLQDRGFKVALVTDGRMSGASGKIPAAIHV+PEAQ GG LARVRD
Sbjct: 481 SNGMPELHKMTPFLGVLQDRGFKVALVTDGRMSGASGKIPAAIHVNPEAQSGGPLARVRD 540

Query: 541 GDIIRVDGVKGTLELKVDADEFAAREPAKGLLGNNVGSGRELFGFMRMAFSSAEQGASAF 600
           GDIIRVDGVKGTLELKVDA+EFAAR PA GLLGNNVG+GRELF FMR+A SSAEQGASAF
Sbjct: 541 GDIIRVDGVKGTLELKVDAEEFAARAPATGLLGNNVGAGRELFAFMRLAASSAEQGASAF 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: 1338
Number of extensions: 46
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 GFF4432 PS417_22690 (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.707946.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 1033.1   0.4          0 1032.9   0.4    1.0  1  FitnessBrowser__WCS417:GFF4432  


Domain annotation for each sequence (and alignments):
>> FitnessBrowser__WCS417:GFF4432  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1032.9   0.4         0         0       1     601 []       2     601 ..       2     601 .. 0.99

  Alignments for each domain:
  == domain 1  score: 1032.9 bits;  conditional E-value: 0
                       TIGR01196   1 hsrlaeiteriierskktrekylekirsaktkgklrstlgcgnlahgvaalsesekvelksekrknlaiitayndmlsa 79 
                                     h+r++e+ter+i+rs++tre+yl+ ir a+  g++r++l c+n+ahgva +  ++k +l+ ++ +n+ai+++yndmlsa
  FitnessBrowser__WCS417:GFF4432   2 HPRVLEVTERLIARSRATREAYLALIRGAAIDGPMRGKLQCANFAHGVAGCGTEDKNSLRMMNAANVAIVSSYNDMLSA 80 
                                     79***************************************************************************** PP

                       TIGR01196  80 hqpfkeypdlikkalqeanavaqvagGvpamcdGvtqGedGmelsllsrdvialstaiglshnmfdgalflGvcdkivp 158
                                     hqp++++p++ikkal+e ++v+q agG+pamcdGvtqGe+Gmelsllsr+via+sta++lshnmfd+al+lG+cdkivp
  FitnessBrowser__WCS417:GFF4432  81 HQPYEHFPEQIKKALREVGSVGQFAGGTPAMCDGVTQGEPGMELSLLSREVIAMSTAVALSHNMFDAALMLGICDKIVP 159
                                     ******************************************************************************* PP

                       TIGR01196 159 GlliaalsfGhlpavfvpaGpmasGlenkekakvrqlfaeGkvdreellksemasyhapGtctfyGtansnqmlvelmG 237
                                     Gl+++al +Ghlp +fvp+Gpm+sG++nk+ka vrq +aeGk++reell+sem+syh+pGtctfyGtan+nq+l+e+mG
  FitnessBrowser__WCS417:GFF4432 160 GLMMGALRYGHLPMIFVPGGPMPSGISNKQKADVRQRYAEGKATREELLESEMKSYHSPGTCTFYGTANTNQLLMEVMG 238
                                     ******************************************************************************* PP

                       TIGR01196 238 lhlpgasfvnpntplrdaltreaakrlarltakngevlplaelideksivnalvgllatGGstnhtlhlvaiaraaGii 316
                                     lhlpgasfvnp+tplrdaltreaa++++rlt  ng+++p++e++deksivn++++l atGGstnhtlh+ aia +aGii
  FitnessBrowser__WCS417:GFF4432 239 LHLPGASFVNPYTPLRDALTREAAHQVTRLTKANGSFMPIGEIVDEKSIVNSIIALNATGGSTNHTLHMPAIAMSAGII 317
                                     ******************************************************************************* PP

                       TIGR01196 317 lnwddlselsdlvpllarvypnGkadvnhfeaaGGlsflirellkeGllhedvetvagkGlrrytkepfledgkleyre 395
                                     l+wdd+ +ls++vp+l +vypnGkad+nhf+aaGG+sflirell++Gllhedv+tvagkGl+ryt+epfl dg+l +re
  FitnessBrowser__WCS417:GFF4432 318 LTWDDMADLSEVVPTLSHVYPNGKADINHFQAAGGMSFLIRELLEAGLLHEDVNTVAGKGLSRYTQEPFLVDGELIWRE 396
                                     ******************************************************************************* PP

                       TIGR01196 396 aaeksldedilrkvdkpfsaeGGlkllkGnlGravikvsavkeesrvieapaivfkdqaellaafkagelerdlvavvr 474
                                     ++ +slde ilr+v + fs+eGGl++++GnlGr+v+kvsav++e++++eapa+vf+dq++l++afkag+le+d+vav+r
  FitnessBrowser__WCS417:GFF4432 397 GPIESLDETILRPVARAFSPEGGLRVMEGNLGRGVMKVSAVAPEHQIVEAPAVVFQDQQDLADAFKAGQLEKDFVAVMR 475
                                     ******************************************************************************* PP

                       TIGR01196 475 fqGpkanGmpelhklttvlGvlqdrgfkvalvtdGrlsGasGkvpaaihvtpealegGalakirdGdlirldavngele 553
                                     fqGp++nGmpelhk+t++lGvlqdrgfkvalvtdGr+sGasGk+paaihv pea++gG+la++rdGd+ir+d+v+g le
  FitnessBrowser__WCS417:GFF4432 476 FQGPRSNGMPELHKMTPFLGVLQDRGFKVALVTDGRMSGASGKIPAAIHVNPEAQSGGPLARVRDGDIIRVDGVKGTLE 554
                                     ******************************************************************************* PP

                       TIGR01196 554 vlvddaelkareleeldlednelGlGrelfaalrekvssaeeGasslt 601
                                     + vd  e++ar +++  l  n++G Grelfa++r ++ssae+Gas++t
  FitnessBrowser__WCS417:GFF4432 555 LKVDAEEFAARAPAT-GLLGNNVGAGRELFAFMRLAASSAEQGASAFT 601
                                     ************776.577789**********************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: 20.88
//
[ok]

This GapMind analysis is from Apr 09 2024. 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:

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 2024 update 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