Alignments for a candidate for edd in Caulobacter crescentus NA1000

GapMind for catabolism of small carbon sources

Alignments for a candidate for edd in Caulobacter crescentus NA1000

Align phosphogluconate dehydratase (EC 4.2.1.12) (characterized)
to candidate CCNA_02134 CCNA_02134 phosphogluconate dehydratase

Query= BRENDA::Q1PAG1
         (608 letters)



>FitnessBrowser__Caulo:CCNA_02134
          Length = 602

 Score =  733 bits (1892), Expect = 0.0
 Identities = 365/600 (60%), Positives = 453/600 (75%), Gaps = 1/600 (0%)

Query: 1   MHPRVLEVTERLVARSRATREAYLALIRGAASDGPQRGKLQCANFAHGVAGCGSEDKHSL 60
           ++P + +VT R+VARS+ +R AYLA +  A  + P R KL CAN+AH  A     DK   
Sbjct: 3   LNPVIADVTARIVARSKDSRAAYLANMDRAIENQPGRAKLSCANWAHAFAASPGVDKLRA 62

Query: 61  RMMNAANVAIVSSYNDMLSAHQPYEHFPEQIKKALREMGSVGQFAGGTPAMCDGVTQGEA 120
              NA N+ IVS+YNDMLSAHQP E +P  IK A R++G+  QFAGG PAMCDGVTQG  
Sbjct: 63  LDPNAPNIGIVSAYNDMLSAHQPLEAYPALIKDAARDVGATAQFAGGVPAMCDGVTQGRP 122

Query: 121 GMELSLPSREVIALSTAVALSHNMFDAALMLGICDKIVPGLMMGALRFGHLPTIFVPGGP 180
           GMELSL SR+VIA++TAVAL+H+ FD+AL LG+CDKIVPGL++GAL F HLP +FVP GP
Sbjct: 123 GMELSLFSRDVIAMATAVALTHDAFDSALYLGVCDKIVPGLVIGALTFSHLPALFVPAGP 182

Query: 181 MPSGISNKEKADVRQRYAEGKATREELLESEMKSYHSPGTCTFYGTANTNQLLMEVMGLH 240
           M SG+ N EKA +R  YAEGK  REELL +E  SYH PGTCTFYGTANTNQ+LME+MG H
Sbjct: 183 MTSGLPNSEKARIRALYAEGKVGREELLAAESASYHGPGTCTFYGTANTNQMLMELMGFH 242

Query: 241 LPGASFVNPYTPLRDALTHEAAQQVTRLTKQSGNFTPIGEIVDERSLVNSIVALHATGGS 300
           LPG++FV+P TPLR+AL  E+A++V  +T +   F P+G ++DE+S VN +V L ATGGS
Sbjct: 243 LPGSAFVHPNTPLREALVKESARRVAAVTNKGNEFIPVGRMIDEKSFVNGVVGLMATGGS 302

Query: 301 TNHTLHMPAIAQAAGIQLTWQDMADLSEVVPTLSHVYPNGKADINHFQAAGGMAFLIREL 360
           TN  LH+ A+A AAG+QLT +D+ D+S+  P L+ VYPNG AD+NHFQAAGGMAF+IREL
Sbjct: 303 TNLALHIIAMAAAAGVQLTLEDLDDISKATPLLARVYPNGSADVNHFQAAGGMAFVIREL 362

Query: 361 LEAGLLHEDVNTVAGRGLSRYTQEPFLDNGKLVWRDGPIESLDENILRPVARAFSPEGGL 420
           L+AGL+HEDV T+AG GLS Y +EP L++G L WRDG  ESLD  I+RPV+  FS EGGL
Sbjct: 363 LKAGLVHEDVQTIAGAGLSLYAKEPVLEDGMLTWRDGAHESLDPAIVRPVSDPFSKEGGL 422

Query: 421 RVMEGNLGRGVMKVSAVALQHQIVEAPAVVFQDQQDLADAFKAGELEKDFVAVMRFQGPR 480
           R+M GNLGRGVMK+SAV  +H ++EAP  VFQ+Q+D   AFK GEL++D V V+RFQGP 
Sbjct: 423 RLMAGNLGRGVMKISAVKPEHHVIEAPCAVFQEQEDFIAAFKRGELDRDVVVVVRFQGPS 482

Query: 481 SNGMPELHKMTPFLGVLQDRGFKVALVTDGRMSGASGKIPAAIHVSPEAQVGGALARVRD 540
           +NGMPELH ++P + VL DRG KVALVTDGRMSGASGK PAAIHV+PEA  GG LA V+D
Sbjct: 483 ANGMPELHNLSPSISVLLDRGHKVALVTDGRMSGASGKTPAAIHVTPEAAKGGPLAYVQD 542

Query: 541 GDIIRVDGVKGTLELKVDADEFAAREPAKGLLGNNVGSGRELFGFMRMAFSSAEQGASAF 600
           GD+IRV+   G L++ VD     AR PA  +  +  G GRELFG+MR    +A+ GAS F
Sbjct: 543 GDVIRVNAETGELKIMVDEATLLARTPA-NVPASKPGFGRELFGWMRSGVGAADAGASVF 601


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: 1092
Number of extensions: 51
Number of successful extensions: 2
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: 602
Length adjustment: 37
Effective length of query: 571
Effective length of database: 565
Effective search space:   322615
Effective search space used:   322615
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 CCNA_02134 CCNA_02134 (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.31212.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   7.9e-297  971.3   0.5   8.8e-297  971.2   0.5    1.0  1  lcl|FitnessBrowser__Caulo:CCNA_02134  CCNA_02134 phosphogluconate dehy


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Caulo:CCNA_02134  CCNA_02134 phosphogluconate dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  971.2   0.5  8.8e-297  8.8e-297       2     600 ..       5     601 ..       4     602 .] 0.99

  Alignments for each domain:
  == domain 1  score: 971.2 bits;  conditional E-value: 8.8e-297
                             TIGR01196   2 srlaeiteriierskktrekylekirsaktkgklrstlgcgnlahgvaalsesekvelksekrknlaiitayn 74 
                                           + +a++t+ri++rsk+ r +yl+++  a ++ + r++l+c+n ah++aa +  +k+     + +n++i++ayn
  lcl|FitnessBrowser__Caulo:CCNA_02134   5 PVIADVTARIVARSKDSRAAYLANMDRAIENQPGRAKLSCANWAHAFAASPGVDKLRALDPNAPNIGIVSAYN 77 
                                           56899******************************************************************** PP

                             TIGR01196  75 dmlsahqpfkeypdlikkalqeanavaqvagGvpamcdGvtqGedGmelsllsrdvialstaiglshnmfdga 147
                                           dmlsahqp++ yp+lik+a+++ +a+aq agGvpamcdGvtqG++Gmelsl+srdvia++ta++l+h+ fd+a
  lcl|FitnessBrowser__Caulo:CCNA_02134  78 DMLSAHQPLEAYPALIKDAARDVGATAQFAGGVPAMCDGVTQGRPGMELSLFSRDVIAMATAVALTHDAFDSA 150
                                           ************************************************************************* PP

                             TIGR01196 148 lflGvcdkivpGlliaalsfGhlpavfvpaGpmasGlenkekakvrqlfaeGkvdreellksemasyhapGtc 220
                                           l+lGvcdkivpGl+i+al+f hlpa+fvpaGpm+sGl+n+eka++r l+aeGkv+reell++e+asyh+pGtc
  lcl|FitnessBrowser__Caulo:CCNA_02134 151 LYLGVCDKIVPGLVIGALTFSHLPALFVPAGPMTSGLPNSEKARIRALYAEGKVGREELLAAESASYHGPGTC 223
                                           ************************************************************************* PP

                             TIGR01196 221 tfyGtansnqmlvelmGlhlpgasfvnpntplrdaltreaakrlarltakngevlplaelideksivnalvgl 293
                                           tfyGtan+nqml+elmG+hlpg++fv+pntplr+al++e+a+r+a++t+k++e++p++++ideks+vn++vgl
  lcl|FitnessBrowser__Caulo:CCNA_02134 224 TFYGTANTNQMLMELMGFHLPGSAFVHPNTPLREALVKESARRVAAVTNKGNEFIPVGRMIDEKSFVNGVVGL 296
                                           ************************************************************************* PP

                             TIGR01196 294 latGGstnhtlhlvaiaraaGiilnwddlselsdlvpllarvypnGkadvnhfeaaGGlsflirellkeGllh 366
                                           +atGGstn +lh++a+a aaG++l+ +dl+++s+  pllarvypnG+advnhf+aaGG++f+irellk+Gl+h
  lcl|FitnessBrowser__Caulo:CCNA_02134 297 MATGGSTNLALHIIAMAAAAGVQLTLEDLDDISKATPLLARVYPNGSADVNHFQAAGGMAFVIRELLKAGLVH 369
                                           ************************************************************************* PP

                             TIGR01196 367 edvetvagkGlrrytkepfledgkleyreaaeksldedilrkvdkpfsaeGGlkllkGnlGravikvsavkee 439
                                           edv+t+ag Gl+ y+kep+ledg l++r++a++sld +i+r+v++pfs+eGGl+l+ GnlGr+v+k+savk+e
  lcl|FitnessBrowser__Caulo:CCNA_02134 370 EDVQTIAGAGLSLYAKEPVLEDGMLTWRDGAHESLDPAIVRPVSDPFSKEGGLRLMAGNLGRGVMKISAVKPE 442
                                           ************************************************************************* PP

                             TIGR01196 440 srvieapaivfkdqaellaafkagelerdlvavvrfqGpkanGmpelhklttvlGvlqdrgfkvalvtdGrls 512
                                           ++vieap+ vf++q++++aafk+gel+rd+v+vvrfqGp anGmpelh l + + vl+drg+kvalvtdGr+s
  lcl|FitnessBrowser__Caulo:CCNA_02134 443 HHVIEAPCAVFQEQEDFIAAFKRGELDRDVVVVVRFQGPSANGMPELHNLSPSISVLLDRGHKVALVTDGRMS 515
                                           ************************************************************************* PP

                             TIGR01196 513 GasGkvpaaihvtpealegGalakirdGdlirldavngelevlvddaelkareleeldlednelGlGrelfaa 585
                                           GasGk paaihvtpea++gG+la ++dGd+ir++a +gel+++vd+a l ar+++++   +++ G Grelf  
  lcl|FitnessBrowser__Caulo:CCNA_02134 516 GASGKTPAAIHVTPEAAKGGPLAYVQDGDVIRVNAETGELKIMVDEATLLARTPANV--PASKPGFGRELFGW 586
                                           *****************************************************8766..5667799******* PP

                             TIGR01196 586 lrekvssaeeGassl 600
                                           +r+ v++a+ Gas++
  lcl|FitnessBrowser__Caulo:CCNA_02134 587 MRSGVGAADAGASVF 601
                                           ************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (601 nodes)
Target sequences:                          1  (602 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: 00:00:00.02
# Mc/sec: 12.37
//
[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