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_RS37440 RR42_RS37440 phosphogluconate dehydratase

Query= BRENDA::Q1PAG1
         (608 letters)



>FitnessBrowser__Cup4G11:RR42_RS37440
          Length = 608

 Score =  736 bits (1901), Expect = 0.0
 Identities = 370/597 (61%), Positives = 448/597 (75%), Gaps = 1/597 (0%)

Query: 2   HPRVLEVTERLVARSRATREAYLALIRGAASDGPQRGKLQCANFAHGVAGCGSEDKHSLR 61
           HP +  VT R+VARS ATR+ Y+   R  A    +R +L C N AH VA    + K  L+
Sbjct: 4   HPVLERVTARIVARSAATRQTYMDRTRAMAGQKVERAQLSCTNLAHAVAAMPEQAKIRLK 63

Query: 62  MMNAANVAIVSSYNDMLSAHQPYEHFPEQIKKALREMGSVGQFAGGTPAMCDGVTQGEAG 121
                N+AIVSSYNDMLSAHQP   +P+ +K+A  E G   QFAGGTPAMCDGVTQG+ G
Sbjct: 64  AQERPNLAIVSSYNDMLSAHQPLAEYPQWLKEAALEAGGTAQFAGGTPAMCDGVTQGQDG 123

Query: 122 MELSLPSREVIALSTAVALSHNMFDAALMLGICDKIVPGLMMGALRFGHLPTIFVPGGPM 181
           M+LSL SR+VIALSTAVALSH MFD AL LG+CDKIVPGL+MGAL FGHLP IFVPGGPM
Sbjct: 124 MDLSLFSRDVIALSTAVALSHQMFDGALYLGVCDKIVPGLVMGALSFGHLPAIFVPGGPM 183

Query: 182 PSGISNKEKADVRQRYAEGKATREELLESEMKSYHSPGTCTFYGTANTNQLLMEVMGLHL 241
            +GI N+EKA VRQRYAEGK +R ELLE+E +SYH PGTCTFYGTAN+NQ+LME+MGLHL
Sbjct: 184 TTGIGNEEKARVRQRYAEGKLSRAELLEAESQSYHGPGTCTFYGTANSNQMLMEIMGLHL 243

Query: 242 PGASFVNPYTPLRDALTHEAAQQVTRLTKQSGNFTPIGEIVDERSLVNSIVALHATGGST 301
           PG +FVNP TPLR+ALT E+A+Q  RL      +TP+ +++DER+ VN IV L ATGGST
Sbjct: 244 PGTAFVNPNTPLREALTRESARQALRLVHGGDRYTPVADVLDERAFVNGIVGLLATGGST 303

Query: 302 NHTLHMPAIAQAAGIQLTWQDMADLSEVVPTLSHVYPNGKADINHFQAAGGMAFLIRELL 361
           NHTLH+ A+A+ AGI L W D A+LSEVVP L+ VYPNG AD+N FQAAGG+  +IR LL
Sbjct: 304 NHTLHLVAMARTAGIMLGWDDFAELSEVVPLLARVYPNGSADVNQFQAAGGLGLVIRGLL 363

Query: 362 EAGLLHEDVNTVAGRGLSRYTQEPFLDNGKLVWRDGPIESLDENILRPVARAFSPEGGLR 421
           + GLLH+DV TV G+GL+ YT+EP L +G+L W DGP   LD+ I+R   + F+PEGG+R
Sbjct: 364 QLGLLHDDVTTVVGKGLADYTREPVLRDGQLTWIDGPEAPLDDTIVRAAGQPFAPEGGIR 423

Query: 422 VMEGNLGRGVMKVSAVALQHQIVEAPAVVFQDQQDLADAFKAGELEKDFVAVMRFQGPRS 481
           +++GN+GR V+K+SAV  +H IV+APA+VF  Q  L +AFK GELE+DFVAV+ +QGP +
Sbjct: 424 LLDGNIGRAVLKISAVKPEHHIVQAPAMVFHTQDALIEAFKRGELERDFVAVLPWQGPAA 483

Query: 482 NGMPELHKMTPFLGVLQDRGFKVALVTDGRMSGASGKIPAAIHVSPEAQVGGALARVRDG 541
            GMPELHK+TP L VLQDRGF VALVTDGRMSGASGK+PAAIHV PEA  GG +ARVRDG
Sbjct: 484 CGMPELHKLTPTLTVLQDRGFHVALVTDGRMSGASGKVPAAIHVCPEALSGGGIARVRDG 543

Query: 542 DIIRVDGVKGTLELKVDADEFAARE-PAKGLLGNNVGSGRELFGFMRMAFSSAEQGA 597
           D +RVD   G L + V   E+AAR      L  N  G GR+LF   R   S+AE GA
Sbjct: 544 DPMRVDAHAGVLTVLVPQAEWAARSVTPPDLSANRHGVGRDLFANFRRHVSTAEAGA 600


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: 1142
Number of extensions: 54
Number of successful extensions: 1
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: 608
Length adjustment: 37
Effective length of query: 571
Effective length of database: 571
Effective search space:   326041
Effective search space used:   326041
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_RS37440 RR42_RS37440 (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.4431.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.7e-308 1009.2   0.0   3.1e-308 1009.0   0.0    1.0  1  lcl|FitnessBrowser__Cup4G11:RR42_RS37440  RR42_RS37440 phosphogluconate de


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cup4G11:RR42_RS37440  RR42_RS37440 phosphogluconate dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1009.0   0.0  3.1e-308  3.1e-308       1     600 [.       4     603 ..       4     604 .. 1.00

  Alignments for each domain:
  == domain 1  score: 1009.0 bits;  conditional E-value: 3.1e-308
                                 TIGR01196   1 hsrlaeiteriierskktrekylekirsaktkgklrstlgcgnlahgvaalsesekvelksekrknlai 69 
                                               h+ l+++t+ri++rs++tr++y+++ r+ + + + r++l+c+nlah+vaa++e+ k+ lk ++r+nlai
  lcl|FitnessBrowser__Cup4G11:RR42_RS37440   4 HPVLERVTARIVARSAATRQTYMDRTRAMAGQKVERAQLSCTNLAHAVAAMPEQAKIRLKAQERPNLAI 72 
                                               67899**************************************************************** PP

                                 TIGR01196  70 itayndmlsahqpfkeypdlikkalqeanavaqvagGvpamcdGvtqGedGmelsllsrdvialstaig 138
                                               +++yndmlsahqp++eyp+ +k+a+ ea+++aq agG+pamcdGvtqG+dGm+lsl+srdvialsta++
  lcl|FitnessBrowser__Cup4G11:RR42_RS37440  73 VSSYNDMLSAHQPLAEYPQWLKEAALEAGGTAQFAGGTPAMCDGVTQGQDGMDLSLFSRDVIALSTAVA 141
                                               ********************************************************************* PP

                                 TIGR01196 139 lshnmfdgalflGvcdkivpGlliaalsfGhlpavfvpaGpmasGlenkekakvrqlfaeGkvdreell 207
                                               lsh+mfdgal+lGvcdkivpGl+++alsfGhlpa+fvp+Gpm++G+ n+eka+vrq +aeGk++r ell
  lcl|FitnessBrowser__Cup4G11:RR42_RS37440 142 LSHQMFDGALYLGVCDKIVPGLVMGALSFGHLPAIFVPGGPMTTGIGNEEKARVRQRYAEGKLSRAELL 210
                                               ********************************************************************* PP

                                 TIGR01196 208 ksemasyhapGtctfyGtansnqmlvelmGlhlpgasfvnpntplrdaltreaakrlarltakngevlp 276
                                               ++e++syh+pGtctfyGtansnqml+e+mGlhlpg++fvnpntplr+altre+a+++ rl+  +++++p
  lcl|FitnessBrowser__Cup4G11:RR42_RS37440 211 EAESQSYHGPGTCTFYGTANSNQMLMEIMGLHLPGTAFVNPNTPLREALTRESARQALRLVHGGDRYTP 279
                                               ********************************************************************* PP

                                 TIGR01196 277 laelideksivnalvgllatGGstnhtlhlvaiaraaGiilnwddlselsdlvpllarvypnGkadvnh 345
                                               +a+++de+++vn++vgllatGGstnhtlhlva+ar+aGi+l wdd+ els++vpllarvypnG+advn+
  lcl|FitnessBrowser__Cup4G11:RR42_RS37440 280 VADVLDERAFVNGIVGLLATGGSTNHTLHLVAMARTAGIMLGWDDFAELSEVVPLLARVYPNGSADVNQ 348
                                               ********************************************************************* PP

                                 TIGR01196 346 feaaGGlsflirellkeGllhedvetvagkGlrrytkepfledgkleyreaaeksldedilrkvdkpfs 414
                                               f+aaGGl+++ir ll+ Gllh+dv+tv+gkGl  yt+ep+l+dg+l++ +++e+ ld+ i+r++ +pf+
  lcl|FitnessBrowser__Cup4G11:RR42_RS37440 349 FQAAGGLGLVIRGLLQLGLLHDDVTTVVGKGLADYTREPVLRDGQLTWIDGPEAPLDDTIVRAAGQPFA 417
                                               ********************************************************************* PP

                                 TIGR01196 415 aeGGlkllkGnlGravikvsavkeesrvieapaivfkdqaellaafkagelerdlvavvrfqGpkanGm 483
                                               +eGG++ll+Gn+Grav+k+savk+e+++++apa+vf++q  l++afk+gelerd+vav+++qGp a Gm
  lcl|FitnessBrowser__Cup4G11:RR42_RS37440 418 PEGGIRLLDGNIGRAVLKISAVKPEHHIVQAPAMVFHTQDALIEAFKRGELERDFVAVLPWQGPAACGM 486
                                               ********************************************************************* PP

                                 TIGR01196 484 pelhklttvlGvlqdrgfkvalvtdGrlsGasGkvpaaihvtpealegGalakirdGdlirldavngel 552
                                               pelhklt++l vlqdrgf valvtdGr+sGasGkvpaaihv+peal+gG +a++rdGd +r+da +g l
  lcl|FitnessBrowser__Cup4G11:RR42_RS37440 487 PELHKLTPTLTVLQDRGFHVALVTDGRMSGASGKVPAAIHVCPEALSGGGIARVRDGDPMRVDAHAGVL 555
                                               ********************************************************************* PP

                                 TIGR01196 553 evlvddaelkareleeldlednelGlGrelfaalrekvssaeeGassl 600
                                               +vlv +ae++ar+++ +dl++n+ G+Gr+lfa++r++vs+ae Ga+sl
  lcl|FitnessBrowser__Cup4G11:RR42_RS37440 556 TVLVPQAEWAARSVTPPDLSANRHGVGRDLFANFRRHVSTAEAGACSL 603
                                               **********************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (601 nodes)
Target sequences:                          1  (608 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: 00:00:00.03
# Mc/sec: 9.75
//
[ok]

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

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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 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