Alignments for a candidate for edd in Rhodanobacter denitrificans 2APBS1

GapMind for catabolism of small carbon sources

Alignments for a candidate for edd in Rhodanobacter denitrificans 2APBS1

Align phosphogluconate dehydratase (EC 4.2.1.12) (characterized)
to candidate WP_015446444.1 R2APBS1_RS00620 phosphogluconate dehydratase

Query= BRENDA::Q1PAG1
         (608 letters)



>NCBI__GCF_000230695.2:WP_015446444.1
          Length = 605

 Score =  724 bits (1870), Expect = 0.0
 Identities = 363/599 (60%), Positives = 446/599 (74%), Gaps = 2/599 (0%)

Query: 1   MHPRVLEVTERLVARSRATREAYLALIRGAASDGPQRGKLQCANFAHGVAGCGSEDKHSL 60
           +HP V EVTERL  RSR TR AYL  I      GPQR  L C N AHG A CGSEDK +L
Sbjct: 4   LHPVVAEVTERLRERSRDTRAAYLRRIDAVDRSGPQREHLSCGNLAHGFAACGSEDKAAL 63

Query: 61  RMMNAANVAIVSSYNDMLSAHQPYEHFPEQIKKALREMGSVGQFAGGTPAMCDGVTQGEA 120
           R    AN+AIV++YNDMLSAHQPYE +P  I++  R+ G   Q AGG PAMCDG+TQG  
Sbjct: 64  RSGRRANLAIVTAYNDMLSAHQPYERYPALIRQVARDAGFTAQVAGGVPAMCDGITQGRP 123

Query: 121 GMELSLPSREVIALSTAVALSHNMFDAALMLGICDKIVPGLMMGALRFGHLPTIFVPGGP 180
           GM+LSL SR+V+AL+TAVALSH+MFD AL LGICDKIVPGL++GAL FGHL   FVP GP
Sbjct: 124 GMQLSLFSRDVVALATAVALSHDMFDGALFLGICDKIVPGLLIGALSFGHLAGAFVPSGP 183

Query: 181 MPSGISNKEKADVRQRYAEGKATREELLESEMKSYHSPGTCTFYGTANTNQLLMEVMGLH 240
           MPSGI N++K+ VRQ +A+GKA++ ELLE+E  SYH+PGTCTFYGTAN+NQ+LME+MGLH
Sbjct: 184 MPSGIPNEQKSKVRQAFADGKASKAELLEAEAASYHAPGTCTFYGTANSNQMLMEIMGLH 243

Query: 241 LPGASFVNPYTPLRDALTHEAAQQVTRLTKQSGNFTPIGEIVDERSLVNSIVALHATGGS 300
           LPGASF  P TPLRDALT E  ++V   +       P+G I+DER+++N ++ LHATGGS
Sbjct: 244 LPGASFTAPDTPLRDALTAEVVRRVAAHSALGDASLPLGHIIDERAIINGVIGLHATGGS 303

Query: 301 TNHTLHMPAIAQAAGIQLTWQDMADLSEVVPTLSHVYPNGKADINHFQAAGGMAFLIREL 360
           TNH LH+ AIA AAGIQL W D   LS V+P L+ VYPNG AD+N F  AGGMAFLI +L
Sbjct: 304 TNHLLHLVAIAHAAGIQLRWDDFDALSGVIPLLARVYPNGYADVNQFHDAGGMAFLIDQL 363

Query: 361 LEAGLLHEDVNTVAGRGLSRYTQEPFLD-NGKLVWRDGPIESLDENILRPVARAFSPEGG 419
           L AGLLH DV T+ G GL  Y Q P LD  G L W+    +S +  +LR V   F P+GG
Sbjct: 364 LGAGLLHADVQTIFGTGLDGYAQVPALDAGGALHWQPVAKQSGNRGVLRGVDEPFRPDGG 423

Query: 420 LRVMEGNLGRGVMKVSAVALQHQIVEAPAVVFQDQQDLADAFKAGELEKDFVAVMRFQGP 479
           LR+++GNLGR V+KVS+V     ++EAPA+VF DQ ++A AFK GEL +DFVAV+RFQGP
Sbjct: 424 LRMLDGNLGRAVIKVSSVPDDRLLIEAPAIVFDDQDEVAGAFKRGELNRDFVAVVRFQGP 483

Query: 480 RSNGMPELHKMTPFLGVLQDRGFKVALVTDGRMSGASGKIPAAIHVSPEAQVGGALARVR 539
           R+NGMPELHK+TP L +LQDRG ++AL+TDGRMSGASG++PAAIHV+PEA  GG LA++R
Sbjct: 484 RANGMPELHKLTPTLALLQDRGHRIALLTDGRMSGASGRVPAAIHVTPEAVAGGNLAKIR 543

Query: 540 DGDIIRVDGVKGTLELKVDADEFAAREP-AKGLLGNNVGSGRELFGFMRMAFSSAEQGA 597
           DGD+IR+D   G L++ ++A E  AR P    L G + G GRELFG  R A ++A+ GA
Sbjct: 544 DGDMIRLDAANGRLDVLMEAHELDARLPHVADLSGEHSGMGRELFGLFRQAAANADLGA 602


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: 1181
Number of extensions: 52
Number of successful extensions: 4
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: 605
Length adjustment: 37
Effective length of query: 571
Effective length of database: 568
Effective search space:   324328
Effective search space used:   324328
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 WP_015446444.1 R2APBS1_RS00620 (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.672805.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   6.2e-297  971.7   0.1     7e-297  971.5   0.1    1.0  1  NCBI__GCF_000230695.2:WP_015446444.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000230695.2:WP_015446444.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  971.5   0.1    7e-297    7e-297       1     599 [.       5     604 ..       5     605 .] 0.99

  Alignments for each domain:
  == domain 1  score: 971.5 bits;  conditional E-value: 7e-297
                             TIGR01196   1 hsrlaeiteriierskktrekylekirsaktkgklrstlgcgnlahgvaalsesekvelksekrknlaiitay 73 
                                           h+ +ae+ter+ ers++tr +yl +i +  ++g++r++l+cgnlahg+aa+  ++k++l+s +r+nlai+tay
  NCBI__GCF_000230695.2:WP_015446444.1   5 HPVVAEVTERLRERSRDTRAAYLRRIDAVDRSGPQREHLSCGNLAHGFAACGSEDKAALRSGRRANLAIVTAY 77 
                                           67899******************************************************************** PP

                             TIGR01196  74 ndmlsahqpfkeypdlikkalqeanavaqvagGvpamcdGvtqGedGmelsllsrdvialstaiglshnmfdg 146
                                           ndmlsahqp+++yp+li++ +++a+ +aqvagGvpamcdG+tqG++Gm+lsl+srdv+al+ta++lsh+mfdg
  NCBI__GCF_000230695.2:WP_015446444.1  78 NDMLSAHQPYERYPALIRQVARDAGFTAQVAGGVPAMCDGITQGRPGMQLSLFSRDVVALATAVALSHDMFDG 150
                                           ************************************************************************* PP

                             TIGR01196 147 alflGvcdkivpGlliaalsfGhlpavfvpaGpmasGlenkekakvrqlfaeGkvdreellksemasyhapGt 219
                                           alflG+cdkivpGlli+alsfGhl++ fvp+Gpm+sG++n++k+kvrq fa+Gk+++ ell++e+asyhapGt
  NCBI__GCF_000230695.2:WP_015446444.1 151 ALFLGICDKIVPGLLIGALSFGHLAGAFVPSGPMPSGIPNEQKSKVRQAFADGKASKAELLEAEAASYHAPGT 223
                                           ************************************************************************* PP

                             TIGR01196 220 ctfyGtansnqmlvelmGlhlpgasfvnpntplrdaltreaakrlarltakngevlplaelideksivnalvg 292
                                           ctfyGtansnqml+e+mGlhlpgasf  p+tplrdalt+e  +r+a+  a ++  lpl+++ide++i+n+++g
  NCBI__GCF_000230695.2:WP_015446444.1 224 CTFYGTANSNQMLMEIMGLHLPGASFTAPDTPLRDALTAEVVRRVAAHSALGDASLPLGHIIDERAIINGVIG 296
                                           ************************************************************************* PP

                             TIGR01196 293 llatGGstnhtlhlvaiaraaGiilnwddlselsdlvpllarvypnGkadvnhfeaaGGlsflirellkeGll 365
                                           l+atGGstnh lhlvaia+aaGi+l wdd+++ls ++pllarvypnG advn+f+ aGG++fli +ll +Gll
  NCBI__GCF_000230695.2:WP_015446444.1 297 LHATGGSTNHLLHLVAIAHAAGIQLRWDDFDALSGVIPLLARVYPNGYADVNQFHDAGGMAFLIDQLLGAGLL 369
                                           ************************************************************************* PP

                             TIGR01196 366 hedvetvagkGlrrytkepfled.gkleyreaaeksldedilrkvdkpfsaeGGlkllkGnlGravikvsavk 437
                                           h dv+t+ g+Gl  y++ p l+  g l++++ a++s +  +lr vd+pf ++GGl++l+GnlGravikvs+v 
  NCBI__GCF_000230695.2:WP_015446444.1 370 HADVQTIFGTGLDGYAQVPALDAgGALHWQPVAKQSGNRGVLRGVDEPFRPDGGLRMLDGNLGRAVIKVSSVP 442
                                           *********************98789*********************************************** PP

                             TIGR01196 438 eesrvieapaivfkdqaellaafkagelerdlvavvrfqGpkanGmpelhklttvlGvlqdrgfkvalvtdGr 510
                                           ++   ieapaivf+dq e++ afk+gel+rd+vavvrfqGp+anGmpelhklt++l +lqdrg+++al+tdGr
  NCBI__GCF_000230695.2:WP_015446444.1 443 DDRLLIEAPAIVFDDQDEVAGAFKRGELNRDFVAVVRFQGPRANGMPELHKLTPTLALLQDRGHRIALLTDGR 515
                                           ************************************************************************* PP

                             TIGR01196 511 lsGasGkvpaaihvtpealegGalakirdGdlirldavngelevlvddaelkareleeldlednelGlGrelf 583
                                           +sGasG+vpaaihvtpea++gG+lakirdGd+irlda ng+l+vl++  el+ar ++  dl+ ++ G+Grelf
  NCBI__GCF_000230695.2:WP_015446444.1 516 MSGASGRVPAAIHVTPEAVAGGNLAKIRDGDMIRLDAANGRLDVLMEAHELDARLPHVADLSGEHSGMGRELF 588
                                           ************************************************************************* PP

                             TIGR01196 584 aalrekvssaeeGass 599
                                             +r++++ a+ Ga +
  NCBI__GCF_000230695.2:WP_015446444.1 589 GLFRQAAANADLGAGV 604
                                           ************9965 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (601 nodes)
Target sequences:                          1  (605 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 34.44
//
[ok]

This GapMind analysis is from Sep 24 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 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