Alignments for a candidate for edd in Cupriavidus basilensis 4G11

GapMind for catabolism of small carbon sources

Alignments for a candidate for edd in Cupriavidus basilensis 4G11

Align phosphogluconate dehydratase (EC 4.2.1.12) (characterized)
to candidate RR42_RS06125 RR42_RS06125 phosphogluconate dehydratase

Query= BRENDA::Q1PAG1
         (608 letters)



>FitnessBrowser__Cup4G11:RR42_RS06125
          Length = 628

 Score =  724 bits (1868), Expect = 0.0
 Identities = 371/607 (61%), Positives = 458/607 (75%), Gaps = 11/607 (1%)

Query: 1   MHPRVLEVTERLVARSRATREAYLALIRGAASD-GPQRGKLQCANFAHGVAGCGSEDKHS 59
           +H  V  VTER++ARS+ +R AYLA    A  + GP RG L CAN AHG+A   + DK  
Sbjct: 5   LHAEVHAVTERVIARSQRSRAAYLARCERAQQEMGPLRG-LSCANLAHGLAALPAHDKLK 63

Query: 60  LRMMNAANVAIVSSYNDMLSAHQPYEHFPEQIKKALREMGSVGQFAGGTPAMCDGVTQGE 119
           LR+ +AAN+ IV++YNDMLSAHQPYE +P  I++A R +G+V Q AGG PAMCDG+TQG 
Sbjct: 64  LRVEHAANLGIVTAYNDMLSAHQPYERYPGVIREAARAVGAVAQVAGGVPAMCDGITQGN 123

Query: 120 AGMELSLPSREVIALSTAVALSHNMFDAALMLGICDKIVPGLMMGALRFGHLPTIFVPGG 179
           AGMELSL SR+ IA++TAV+LSHN FDAA+MLG+CDKIVPGL+MGAL+FGHLP +FVP G
Sbjct: 124 AGMELSLFSRDAIAMATAVSLSHNTFDAAVMLGVCDKIVPGLLMGALQFGHLPVVFVPAG 183

Query: 180 PMPSGISNKEKADVRQRYAEGKATREELLESEMKSYHSPGTCTFYGTANTNQLLMEVMGL 239
           PM +G+SNKEKA VRQ YA G+  RE LLE+E ++YH  GTCTFYGTAN+NQ LME+MGL
Sbjct: 184 PMSTGLSNKEKARVRQLYATGQVGREALLEAECEAYHGAGTCTFYGTANSNQFLMEIMGL 243

Query: 240 HLPGASFVNPYTPLRDALTHEAAQQVTRLTKQSGNFTPIGEIVDERSLVNSIVALHATGG 299
           H+PGA+FV+P + LRDALT  AAQ+   LT + G++ P+  IVDER+++N++V L ATGG
Sbjct: 244 HMPGAAFVHPDSGLRDALTAAAAQRALALTARGGDYLPLARIVDERAVINAVVGLLATGG 303

Query: 300 STNHTLHMPAIAQAAGIQLTWQDMADLSEVVPTLSHVYPNGKADINHFQAAGGMAFLIRE 359
           STNHT+H+ A+A+AAGI + W D   LS + P L+ VYPNG AD+NHF AAGG+A++IR+
Sbjct: 304 STNHTIHLVAMARAAGILIDWDDFDRLSRITPLLARVYPNGSADVNHFHAAGGVAYVIRQ 363

Query: 360 LLEAGLLHEDVNTVAGRGLSRYTQEPFLDNGKLVWRDGPIESLDENILRPVARAFSPEGG 419
           LL AGLLHEDV TVAGRGL+RYTQEP + +G L WRDG   S D  +L   A  FS EGG
Sbjct: 364 LLSAGLLHEDVETVAGRGLARYTQEPVMIDGVLQWRDGAAVSGDATVLATAAEPFSAEGG 423

Query: 420 LRVMEGNLGRGVMKVSAVALQHQIVEAPAVVFQDQQDLADAFKAGELEKDFVAVMRFQGP 479
           LR+++GNLGRG++KVSAVA +H++VEAPA VF  Q+ L  AF+AGE   D +AV+RFQGP
Sbjct: 424 LRLLQGNLGRGMIKVSAVADEHRVVEAPARVFDSQEQLQAAFEAGEFTGDMIAVVRFQGP 483

Query: 480 RSNGMPELHKMTPFLGVLQDRGFKVALVTDGRMSGASGKIPAAIHVSPEAQVGGALARVR 539
            +NGMPELH++TP LG LQD G KVALVTDGRMSGASGK+PA IHV PEA  GG LARVR
Sbjct: 484 NANGMPELHRLTPVLGSLQDAGHKVALVTDGRMSGASGKVPAVIHVGPEALAGGPLARVR 543

Query: 540 DGDIIRVDGVKGTLELKVDAD---EFAAREPAKGLLGN----NVGSGRELFGFMRMAFSS 592
           DGD IRVD V GTLE    A+   + A R  A  +L +    N   GR LFG  R     
Sbjct: 544 DGDRIRVDAVAGTLEWLGAANGDGDLATR--ASAVLPDDAFANFSVGRGLFGLFRRNARI 601

Query: 593 AEQGASA 599
           AE+G SA
Sbjct: 602 AEEGGSA 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: 1155
Number of extensions: 47
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: 628
Length adjustment: 37
Effective length of query: 571
Effective length of database: 591
Effective search space:   337461
Effective search space used:   337461
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 RR42_RS06125 RR42_RS06125 (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.720.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.7e-291  953.7   3.5     2e-291  953.5   3.5    1.0  1  lcl|FitnessBrowser__Cup4G11:RR42_RS06125  RR42_RS06125 phosphogluconate de


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cup4G11:RR42_RS06125  RR42_RS06125 phosphogluconate dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  953.5   3.5    2e-291    2e-291       1     600 [.       6     609 ..       6     610 .. 0.97

  Alignments for each domain:
  == domain 1  score: 953.5 bits;  conditional E-value: 2e-291
                                 TIGR01196   1 hsrlaeiteriierskktrekylekirsakt.kgklrstlgcgnlahgvaalsesekvelksekrknla 68 
                                               h+++ ++ter+i+rs++ r +yl++ + a++ +g+lr+ l+c+nlahg+aal+ ++k++l+ e+ +nl+
  lcl|FitnessBrowser__Cup4G11:RR42_RS06125   6 HAEVHAVTERVIARSQRSRAAYLARCERAQQeMGPLRG-LSCANLAHGLAALPAHDKLKLRVEHAANLG 73 
                                               678999********************999872567776.****************************** PP

                                 TIGR01196  69 iitayndmlsahqpfkeypdlikkalqeanavaqvagGvpamcdGvtqGedGmelsllsrdvialstai 137
                                               i+tayndmlsahqp+++yp++i++a++  +avaqvagGvpamcdG+tqG++Gmelsl+srd ia++ta+
  lcl|FitnessBrowser__Cup4G11:RR42_RS06125  74 IVTAYNDMLSAHQPYERYPGVIREAARAVGAVAQVAGGVPAMCDGITQGNAGMELSLFSRDAIAMATAV 142
                                               ********************************************************************* PP

                                 TIGR01196 138 glshnmfdgalflGvcdkivpGlliaalsfGhlpavfvpaGpmasGlenkekakvrqlfaeGkvdreel 206
                                               +lshn fd+a++lGvcdkivpGll++al fGhlp vfvpaGpm++Gl+nkeka+vrql+a G+v+re+l
  lcl|FitnessBrowser__Cup4G11:RR42_RS06125 143 SLSHNTFDAAVMLGVCDKIVPGLLMGALQFGHLPVVFVPAGPMSTGLSNKEKARVRQLYATGQVGREAL 211
                                               ********************************************************************* PP

                                 TIGR01196 207 lksemasyhapGtctfyGtansnqmlvelmGlhlpgasfvnpntplrdaltreaakrlarltakngevl 275
                                               l++e ++yh++GtctfyGtansnq+l+e+mGlh+pga+fv+p++ lrdalt++aa+r+ +lta++g++l
  lcl|FitnessBrowser__Cup4G11:RR42_RS06125 212 LEAECEAYHGAGTCTFYGTANSNQFLMEIMGLHMPGAAFVHPDSGLRDALTAAAAQRALALTARGGDYL 280
                                               ********************************************************************* PP

                                 TIGR01196 276 plaelideksivnalvgllatGGstnhtlhlvaiaraaGiilnwddlselsdlvpllarvypnGkadvn 344
                                               pla+++de++++na+vgllatGGstnht+hlva+araaGi+++wdd++ ls + pllarvypnG+advn
  lcl|FitnessBrowser__Cup4G11:RR42_RS06125 281 PLARIVDERAVINAVVGLLATGGSTNHTIHLVAMARAAGILIDWDDFDRLSRITPLLARVYPNGSADVN 349
                                               ********************************************************************* PP

                                 TIGR01196 345 hfeaaGGlsflirellkeGllhedvetvagkGlrrytkepfledgkleyreaaeksldedilrkvdkpf 413
                                               hf+aaGG++++ir+ll++Gllhedvetvag+Gl ryt+ep++ dg l++r++a  s d  +l+++ +pf
  lcl|FitnessBrowser__Cup4G11:RR42_RS06125 350 HFHAAGGVAYVIRQLLSAGLLHEDVETVAGRGLARYTQEPVMIDGVLQWRDGAAVSGDATVLATAAEPF 418
                                               ********************************************************************* PP

                                 TIGR01196 414 saeGGlkllkGnlGravikvsavkeesrvieapaivfkdqaellaafkagelerdlvavvrfqGpkanG 482
                                               saeGGl+ll+GnlGr++ikvsav++e+rv+eapa+vf++q++l+aaf+age+ +d++avvrfqGp+anG
  lcl|FitnessBrowser__Cup4G11:RR42_RS06125 419 SAEGGLRLLQGNLGRGMIKVSAVADEHRVVEAPARVFDSQEQLQAAFEAGEFTGDMIAVVRFQGPNANG 487
                                               ********************************************************************* PP

                                 TIGR01196 483 mpelhklttvlGvlqdrgfkvalvtdGrlsGasGkvpaaihvtpealegGalakirdGdlirldavnge 551
                                               mpelh+lt+vlG lqd g+kvalvtdGr+sGasGkvpa ihv peal+gG+la++rdGd+ir+dav+g 
  lcl|FitnessBrowser__Cup4G11:RR42_RS06125 488 MPELHRLTPVLGSLQDAGHKVALVTDGRMSGASGKVPAVIHVGPEALAGGPLARVRDGDRIRVDAVAGT 556
                                               ********************************************************************* PP

                                 TIGR01196 552 levl...vddaelkareleel.dlednelGlGrelfaalrekvssaeeGassl 600
                                               le l     d +l++r  + l d   +++ +Gr lf  +r+++  aeeG+s+l
  lcl|FitnessBrowser__Cup4G11:RR42_RS06125 557 LEWLgaaNGDGDLATRASAVLpDDAFANFSVGRGLFGLFRRNARIAEEGGSAL 609
                                               **99332346779999877651677799*********************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (601 nodes)
Target sequences:                          1  (628 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: 00:00:00.04
# Mc/sec: 8.90
//
[ok]

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

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Protein sequences (fasta format)
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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 paper from 2022 on GapMind for carbon sources, or view the source code.

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