Alignments for a candidate for edd in Dyella japonica UNC79MFTsu3.2

GapMind for catabolism of small carbon sources

Alignments for a candidate for edd in Dyella japonica UNC79MFTsu3.2

Align phosphogluconate dehydratase (EC 4.2.1.12) (characterized)
to candidate N515DRAFT_3177 N515DRAFT_3177 6-phosphogluconate dehydratase

Query= BRENDA::Q1PAG1
         (608 letters)



>FitnessBrowser__Dyella79:N515DRAFT_3177
          Length = 606

 Score =  749 bits (1934), Expect = 0.0
 Identities = 376/599 (62%), Positives = 455/599 (75%), Gaps = 2/599 (0%)

Query: 1   MHPRVLEVTERLVARSRATREAYLALIRGAASDGPQRGKLQCANFAHGVAGCGSEDKHSL 60
           +HP V EVT RL  RSR TR AYLA I  A + G  R +L C N AHG A CG  DK +L
Sbjct: 5   LHPVVAEVTARLRERSRDTRAAYLARIAAAGTGGTHRERLSCGNLAHGFAACGPHDKAAL 64

Query: 61  RMMNAANVAIVSSYNDMLSAHQPYEHFPEQIKKALREMGSVGQFAGGTPAMCDGVTQGEA 120
           R  +  N+ IV+SYNDMLSAHQPYE +PE I++  RE G   Q AGG PAMCDGVTQG  
Sbjct: 65  REGHTPNLGIVTSYNDMLSAHQPYERYPELIRRIARESGITAQVAGGVPAMCDGVTQGRE 124

Query: 121 GMELSLPSREVIALSTAVALSHNMFDAALMLGICDKIVPGLMMGALRFGHLPTIFVPGGP 180
           GMELSL SR++IA++TAV+LSH+MFD  L LGICDKIVPGL++GAL FGHLP IFVPGGP
Sbjct: 125 GMELSLFSRDLIAMATAVSLSHDMFDGTLYLGICDKIVPGLLIGALSFGHLPGIFVPGGP 184

Query: 181 MPSGISNKEKADVRQRYAEGKATREELLESEMKSYHSPGTCTFYGTANTNQLLMEVMGLH 240
           MPSGI+N++K+ VRQ YAEGKA R ELLE+E  +YH+PGTCTFYGTAN+NQ+LME+MGLH
Sbjct: 185 MPSGITNEQKSKVRQAYAEGKANRAELLEAEAAAYHAPGTCTFYGTANSNQMLMEIMGLH 244

Query: 241 LPGASFVNPYTPLRDALTHEAAQQVTRLTKQSGNFTPIGEIVDERSLVNSIVALHATGGS 300
           LPGASFV P TPLRDALT EA  +V  L+    N  PIG IVDER+++N ++ LHATGGS
Sbjct: 245 LPGASFVAPDTPLRDALTAEAVHRVAALSAHGDNHLPIGHIVDERAIINGVIGLHATGGS 304

Query: 301 TNHTLHMPAIAQAAGIQLTWQDMADLSEVVPTLSHVYPNGKADINHFQAAGGMAFLIREL 360
           TNH LH+ A+A+AAGIQL W D   LS VVP L+ VYPNG AD+N F  AGGMAFLI +L
Sbjct: 305 TNHLLHLVAMARAAGIQLRWDDFDALSSVVPLLARVYPNGYADVNQFHDAGGMAFLIDQL 364

Query: 361 LEAGLLHEDVNTVAGRGLSRYTQEPFLD-NGKLVWRDGPIESLDENILRPVARAFSPEGG 419
           L AGLLH DV TV G GL  Y Q P LD +G L W     ES +  +LR +A  F  +GG
Sbjct: 365 LGAGLLHGDVRTVFGTGLDGYAQVPSLDASGALQWTPVAKESGNRGVLRGMAEPFRADGG 424

Query: 420 LRVMEGNLGRGVMKVSAVALQHQIVEAPAVVFQDQQDLADAFKAGELEKDFVAVMRFQGP 479
           LR++ GNLGR V+KVS+V    Q++EAPAVVF DQ ++  AF+ GEL +DF+AV+RFQGP
Sbjct: 425 LRMLAGNLGRAVIKVSSVPDDRQVIEAPAVVFHDQDEVRKAFERGELNRDFIAVVRFQGP 484

Query: 480 RSNGMPELHKMTPFLGVLQDRGFKVALVTDGRMSGASGKIPAAIHVSPEAQVGGALARVR 539
           R+ GMPELHK+TP L VLQDRG+++AL+TDGRMSGASG++PAAIHV+PEAQ  GA+AR+R
Sbjct: 485 RAIGMPELHKLTPTLAVLQDRGYRIALLTDGRMSGASGRVPAAIHVTPEAQAQGAIARIR 544

Query: 540 DGDIIRVDGVKGTLELKVDADEFAAREPAKG-LLGNNVGSGRELFGFMRMAFSSAEQGA 597
           DGD+IR+D  +GTL++ VDA EFA+R PA   L  ++ G GRELFG  R A + A+ GA
Sbjct: 545 DGDLIRLDATRGTLDVLVDASEFASRAPATADLSSHHSGMGRELFGLFRQAAAEADLGA 603


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: 1137
Number of extensions: 60
Number of successful extensions: 3
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: 606
Length adjustment: 37
Effective length of query: 571
Effective length of database: 569
Effective search space:   324899
Effective search space used:   324899
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 N515DRAFT_3177 N515DRAFT_3177 (6-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.16059.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
   1.1e-300  984.1   0.1   1.2e-300  983.9   0.1    1.0  1  lcl|FitnessBrowser__Dyella79:N515DRAFT_3177  N515DRAFT_3177 6-phosphogluconat


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dyella79:N515DRAFT_3177  N515DRAFT_3177 6-phosphogluconate dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  983.9   0.1  1.2e-300  1.2e-300       1     599 [.       6     605 ..       6     606 .] 0.99

  Alignments for each domain:
  == domain 1  score: 983.9 bits;  conditional E-value: 1.2e-300
                                    TIGR01196   1 hsrlaeiteriierskktrekylekirsaktkgklrstlgcgnlahgvaalsesekvelksekrkn 66 
                                                  h+ +ae+t+r+ ers++tr +yl++i +a t g++r++l+cgnlahg+aa+ +++k++l++ + +n
  lcl|FitnessBrowser__Dyella79:N515DRAFT_3177   6 HPVVAEVTARLRERSRDTRAAYLARIAAAGTGGTHRERLSCGNLAHGFAACGPHDKAALREGHTPN 71 
                                                  67899************************************************************* PP

                                    TIGR01196  67 laiitayndmlsahqpfkeypdlikkalqeanavaqvagGvpamcdGvtqGedGmelsllsrdvia 132
                                                  l+i+t+yndmlsahqp+++yp+li++ ++e++ +aqvagGvpamcdGvtqG++Gmelsl+srd+ia
  lcl|FitnessBrowser__Dyella79:N515DRAFT_3177  72 LGIVTSYNDMLSAHQPYERYPELIRRIARESGITAQVAGGVPAMCDGVTQGREGMELSLFSRDLIA 137
                                                  ****************************************************************** PP

                                    TIGR01196 133 lstaiglshnmfdgalflGvcdkivpGlliaalsfGhlpavfvpaGpmasGlenkekakvrqlfae 198
                                                  ++ta++lsh+mfdg+l+lG+cdkivpGlli+alsfGhlp++fvp+Gpm+sG++n++k+kvrq +ae
  lcl|FitnessBrowser__Dyella79:N515DRAFT_3177 138 MATAVSLSHDMFDGTLYLGICDKIVPGLLIGALSFGHLPGIFVPGGPMPSGITNEQKSKVRQAYAE 203
                                                  ****************************************************************** PP

                                    TIGR01196 199 GkvdreellksemasyhapGtctfyGtansnqmlvelmGlhlpgasfvnpntplrdaltreaakrl 264
                                                  Gk++r ell++e+a+yhapGtctfyGtansnqml+e+mGlhlpgasfv p+tplrdalt+ea +r+
  lcl|FitnessBrowser__Dyella79:N515DRAFT_3177 204 GKANRAELLEAEAAAYHAPGTCTFYGTANSNQMLMEIMGLHLPGASFVAPDTPLRDALTAEAVHRV 269
                                                  ****************************************************************** PP

                                    TIGR01196 265 arltakngevlplaelideksivnalvgllatGGstnhtlhlvaiaraaGiilnwddlselsdlvp 330
                                                  a+l a++++ lp+++++de++i+n+++gl+atGGstnh lhlva+araaGi+l wdd+++ls++vp
  lcl|FitnessBrowser__Dyella79:N515DRAFT_3177 270 AALSAHGDNHLPIGHIVDERAIINGVIGLHATGGSTNHLLHLVAMARAAGIQLRWDDFDALSSVVP 335
                                                  ****************************************************************** PP

                                    TIGR01196 331 llarvypnGkadvnhfeaaGGlsflirellkeGllhedvetvagkGlrrytkepfled.gkleyre 395
                                                  llarvypnG advn+f+ aGG++fli +ll +Gllh dv+tv g+Gl  y++ p l+  g l++ +
  lcl|FitnessBrowser__Dyella79:N515DRAFT_3177 336 LLARVYPNGYADVNQFHDAGGMAFLIDQLLGAGLLHGDVRTVFGTGLDGYAQVPSLDAsGALQWTP 401
                                                  ********************************************************9779****** PP

                                    TIGR01196 396 aaeksldedilrkvdkpfsaeGGlkllkGnlGravikvsavkeesrvieapaivfkdqaellaafk 461
                                                   a++s +  +lr + +pf a+GGl++l GnlGravikvs+v ++ +vieapa+vf+dq e+ +af+
  lcl|FitnessBrowser__Dyella79:N515DRAFT_3177 402 VAKESGNRGVLRGMAEPFRADGGLRMLAGNLGRAVIKVSSVPDDRQVIEAPAVVFHDQDEVRKAFE 467
                                                  ****************************************************************** PP

                                    TIGR01196 462 agelerdlvavvrfqGpkanGmpelhklttvlGvlqdrgfkvalvtdGrlsGasGkvpaaihvtpe 527
                                                  +gel+rd++avvrfqGp+a Gmpelhklt++l vlqdrg+++al+tdGr+sGasG+vpaaihvtpe
  lcl|FitnessBrowser__Dyella79:N515DRAFT_3177 468 RGELNRDFIAVVRFQGPRAIGMPELHKLTPTLAVLQDRGYRIALLTDGRMSGASGRVPAAIHVTPE 533
                                                  ****************************************************************** PP

                                    TIGR01196 528 alegGalakirdGdlirldavngelevlvddaelkareleeldlednelGlGrelfaalrekvssa 593
                                                  a+++Ga+a+irdGdlirlda+ g l+vlvd  e+++r +++ dl++ + G+Grelf  +r++++ a
  lcl|FitnessBrowser__Dyella79:N515DRAFT_3177 534 AQAQGAIARIRDGDLIRLDATRGTLDVLVDASEFASRAPATADLSSHHSGMGRELFGLFRQAAAEA 599
                                                  ****************************************************************** PP

                                    TIGR01196 594 eeGass 599
                                                  + Ga +
  lcl|FitnessBrowser__Dyella79:N515DRAFT_3177 600 DLGAGV 605
                                                  *99965 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (601 nodes)
Target sequences:                          1  (606 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 0.01s 00:00:00.04 Elapsed: 00:00:00.05
# Mc/sec: 7.00
//
[ok]

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

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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:

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