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.28424.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: 12.40
//
[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