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.26012.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  lcl|FitnessBrowser__WCS417:GFF4432  PS417_22690 phosphogluconate deh


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__WCS417:GFF4432  PS417_22690 phosphogluconate dehydratase
   #    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 hsrlaeiteriierskktrekylekirsaktkgklrstlgcgnlahgvaalsesekvelksekrknlaiitaynd 75 
                                         h+r++e+ter+i+rs++tre+yl+ ir a+  g++r++l c+n+ahgva +  ++k +l+ ++ +n+ai+++ynd
  lcl|FitnessBrowser__WCS417:GFF4432   2 HPRVLEVTERLIARSRATREAYLALIRGAAIDGPMRGKLQCANFAHGVAGCGTEDKNSLRMMNAANVAIVSSYND 76 
                                         79************************************************************************* PP

                           TIGR01196  76 mlsahqpfkeypdlikkalqeanavaqvagGvpamcdGvtqGedGmelsllsrdvialstaiglshnmfdgalfl 150
                                         mlsahqp++++p++ikkal+e ++v+q agG+pamcdGvtqGe+Gmelsllsr+via+sta++lshnmfd+al+l
  lcl|FitnessBrowser__WCS417:GFF4432  77 MLSAHQPYEHFPEQIKKALREVGSVGQFAGGTPAMCDGVTQGEPGMELSLLSREVIAMSTAVALSHNMFDAALML 151
                                         *************************************************************************** PP

                           TIGR01196 151 GvcdkivpGlliaalsfGhlpavfvpaGpmasGlenkekakvrqlfaeGkvdreellksemasyhapGtctfyGt 225
                                         G+cdkivpGl+++al +Ghlp +fvp+Gpm+sG++nk+ka vrq +aeGk++reell+sem+syh+pGtctfyGt
  lcl|FitnessBrowser__WCS417:GFF4432 152 GICDKIVPGLMMGALRYGHLPMIFVPGGPMPSGISNKQKADVRQRYAEGKATREELLESEMKSYHSPGTCTFYGT 226
                                         *************************************************************************** PP

                           TIGR01196 226 ansnqmlvelmGlhlpgasfvnpntplrdaltreaakrlarltakngevlplaelideksivnalvgllatGGst 300
                                         an+nq+l+e+mGlhlpgasfvnp+tplrdaltreaa++++rlt  ng+++p++e++deksivn++++l atGGst
  lcl|FitnessBrowser__WCS417:GFF4432 227 ANTNQLLMEVMGLHLPGASFVNPYTPLRDALTREAAHQVTRLTKANGSFMPIGEIVDEKSIVNSIIALNATGGST 301
                                         *************************************************************************** PP

                           TIGR01196 301 nhtlhlvaiaraaGiilnwddlselsdlvpllarvypnGkadvnhfeaaGGlsflirellkeGllhedvetvagk 375
                                         nhtlh+ aia +aGiil+wdd+ +ls++vp+l +vypnGkad+nhf+aaGG+sflirell++Gllhedv+tvagk
  lcl|FitnessBrowser__WCS417:GFF4432 302 NHTLHMPAIAMSAGIILTWDDMADLSEVVPTLSHVYPNGKADINHFQAAGGMSFLIRELLEAGLLHEDVNTVAGK 376
                                         *************************************************************************** PP

                           TIGR01196 376 GlrrytkepfledgkleyreaaeksldedilrkvdkpfsaeGGlkllkGnlGravikvsavkeesrvieapaivf 450
                                         Gl+ryt+epfl dg+l +re++ +slde ilr+v + fs+eGGl++++GnlGr+v+kvsav++e++++eapa+vf
  lcl|FitnessBrowser__WCS417:GFF4432 377 GLSRYTQEPFLVDGELIWREGPIESLDETILRPVARAFSPEGGLRVMEGNLGRGVMKVSAVAPEHQIVEAPAVVF 451
                                         *************************************************************************** PP

                           TIGR01196 451 kdqaellaafkagelerdlvavvrfqGpkanGmpelhklttvlGvlqdrgfkvalvtdGrlsGasGkvpaaihvt 525
                                         +dq++l++afkag+le+d+vav+rfqGp++nGmpelhk+t++lGvlqdrgfkvalvtdGr+sGasGk+paaihv 
  lcl|FitnessBrowser__WCS417:GFF4432 452 QDQQDLADAFKAGQLEKDFVAVMRFQGPRSNGMPELHKMTPFLGVLQDRGFKVALVTDGRMSGASGKIPAAIHVN 526
                                         *************************************************************************** PP

                           TIGR01196 526 pealegGalakirdGdlirldavngelevlvddaelkareleeldlednelGlGrelfaalrekvssaeeGassl 600
                                         pea++gG+la++rdGd+ir+d+v+g le+ vd  e++ar +++  l  n++G Grelfa++r ++ssae+Gas++
  lcl|FitnessBrowser__WCS417:GFF4432 527 PEAQSGGPLARVRDGDIIRVDGVKGTLELKVDAEEFAARAPAT-GLLGNNVGAGRELFAFMRLAASSAEQGASAF 600
                                         ****************************************776.577789**********************998 PP

                           TIGR01196 601 t 601
                                         t
  lcl|FitnessBrowser__WCS417:GFF4432 601 T 601
                                         6 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.03
# Mc/sec: 11.20
//
[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:

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