Alignments for a candidate for edd in Stenotrophomonas chelatiphaga DSM 21508

GapMind for catabolism of small carbon sources

Alignments for a candidate for edd in Stenotrophomonas chelatiphaga DSM 21508

Align phosphogluconate dehydratase (EC 4.2.1.12) (characterized)
to candidate WP_057508152.1 ABB28_RS08120 phosphogluconate dehydratase

Query= BRENDA::Q1PAG1
         (608 letters)



>NCBI__GCF_001431535.1:WP_057508152.1
          Length = 638

 Score =  703 bits (1814), Expect = 0.0
 Identities = 351/597 (58%), Positives = 443/597 (74%)

Query: 1   MHPRVLEVTERLVARSRATREAYLALIRGAASDGPQRGKLQCANFAHGVAGCGSEDKHSL 60
           +HP++  +TER+V RS A+R AYLA I  A  DGP R +L C N AHG A CG  DK  L
Sbjct: 3   LHPQLHAITERIVRRSAASRAAYLAGIDAALRDGPFRSRLSCGNLAHGFAACGGTDKKRL 62

Query: 61  RMMNAANVAIVSSYNDMLSAHQPYEHFPEQIKKALREMGSVGQFAGGTPAMCDGVTQGEA 120
           R     N+ I++SYNDMLSAHQP+E +PEQI++  RE G+  Q AGG PAMCDGVTQG  
Sbjct: 63  RGGVTPNLGIITSYNDMLSAHQPFETYPEQIREIAREWGATAQVAGGVPAMCDGVTQGRG 122

Query: 121 GMELSLPSREVIALSTAVALSHNMFDAALMLGICDKIVPGLMMGALRFGHLPTIFVPGGP 180
           GMELSL SR+VIA STA+ LSH+MFDAA+ LG+CDKIVPGL++GAL FGHLP++FVP GP
Sbjct: 123 GMELSLFSRDVIAQSTAIGLSHDMFDAAIYLGVCDKIVPGLLIGALAFGHLPSVFVPAGP 182

Query: 181 MPSGISNKEKADVRQRYAEGKATREELLESEMKSYHSPGTCTFYGTANTNQLLMEVMGLH 240
           M  GI NK+KA+VR+RYA G+ATREELLE+E  SYH  GTCTFYGTAN+NQ+L+E MG+ 
Sbjct: 183 MTPGIPNKQKAEVRERYAAGEATREELLEAEAASYHGAGTCTFYGTANSNQVLLEAMGVQ 242

Query: 241 LPGASFVNPYTPLRDALTHEAAQQVTRLTKQSGNFTPIGEIVDERSLVNSIVALHATGGS 300
           LPGASFVNP   LR ALT EA  +   +T    ++ PIG I+DER++VN+IVAL ATGGS
Sbjct: 243 LPGASFVNPEQTLRGALTREATVRALEMTALGDDYRPIGRIIDERAIVNAIVALMATGGS 302

Query: 301 TNHTLHMPAIAQAAGIQLTWQDMADLSEVVPTLSHVYPNGKADINHFQAAGGMAFLIREL 360
           TNHT+H  A+A+AAGI +TW DM  LS+++P L+ VYPNG+AD+N F AAGG AF+  EL
Sbjct: 303 TNHTIHWIAVARAAGIVVTWDDMDQLSQLIPLLTRVYPNGEADVNRFAAAGGPAFVFGEL 362

Query: 361 LEAGLLHEDVNTVAGRGLSRYTQEPFLDNGKLVWRDGPIESLDENILRPVARAFSPEGGL 420
           + AGL+H D+ TVA  G++ Y +EP L +G++ W DG I S DE++ R V   F  +GGL
Sbjct: 363 IRAGLMHGDIVTVARGGMADYAREPRLQDGQVTWVDGIIRSADEDVARGVDNPFESQGGL 422

Query: 421 RVMEGNLGRGVMKVSAVALQHQIVEAPAVVFQDQQDLADAFKAGELEKDFVAVMRFQGPR 480
           R++ GNLGR ++K+SAV  Q++ +EAPAVV    Q L     AG L +DFVAV+R+QGPR
Sbjct: 423 RLLRGNLGRSLIKLSAVKPQYRSIEAPAVVVDAPQVLNKLHAAGLLPQDFVAVVRYQGPR 482

Query: 481 SNGMPELHKMTPFLGVLQDRGFKVALVTDGRMSGASGKIPAAIHVSPEAQVGGALARVRD 540
           +NGMPELH + P LG+LQ++G +VALVTDGR+SGASGKIPAAIH++PEA  GG L ++R+
Sbjct: 483 ANGMPELHSLAPLLGLLQNQGRRVALVTDGRLSGASGKIPAAIHMTPEAARGGPLGKLRE 542

Query: 541 GDIIRVDGVKGTLELKVDADEFAAREPAKGLLGNNVGSGRELFGFMRMAFSSAEQGA 597
           GDIIR+DG  GTLE+ VD  E+AAR  A          GR LF   R+    A+QGA
Sbjct: 543 GDIIRLDGEAGTLEVLVDEAEWAARTHAPNTAPAANDLGRNLFAVNRLVVGPADQGA 599


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: 1180
Number of extensions: 49
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: 638
Length adjustment: 37
Effective length of query: 571
Effective length of database: 601
Effective search space:   343171
Effective search space used:   343171
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: 54 (25.4 bits)

Align candidate WP_057508152.1 ABB28_RS08120 (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.28821.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   7.2e-281  918.6   0.0   8.2e-281  918.4   0.0    1.0  1  lcl|NCBI__GCF_001431535.1:WP_057508152.1  ABB28_RS08120 phosphogluconate d


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_001431535.1:WP_057508152.1  ABB28_RS08120 phosphogluconate dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  918.4   0.0  8.2e-281  8.2e-281       1     600 [.       4     602 ..       4     603 .. 0.99

  Alignments for each domain:
  == domain 1  score: 918.4 bits;  conditional E-value: 8.2e-281
                                 TIGR01196   1 hsrlaeiteriierskktrekylekirsaktkgklrstlgcgnlahgvaalsesekvelksekrknlai 69 
                                               h++l +iteri+ rs++ r +yl+ i +a + g++rs+l+cgnlahg+aa+  ++k  l+    +nl+i
  lcl|NCBI__GCF_001431535.1:WP_057508152.1   4 HPQLHAITERIVRRSAASRAAYLAGIDAALRDGPFRSRLSCGNLAHGFAACGGTDKKRLRGGVTPNLGI 72 
                                               799****************************************************************** PP

                                 TIGR01196  70 itayndmlsahqpfkeypdlikkalqeanavaqvagGvpamcdGvtqGedGmelsllsrdvialstaig 138
                                               it+yndmlsahqpf++yp++i++ ++e +a+aqvagGvpamcdGvtqG+ Gmelsl+srdvia staig
  lcl|NCBI__GCF_001431535.1:WP_057508152.1  73 ITSYNDMLSAHQPFETYPEQIREIAREWGATAQVAGGVPAMCDGVTQGRGGMELSLFSRDVIAQSTAIG 141
                                               ********************************************************************* PP

                                 TIGR01196 139 lshnmfdgalflGvcdkivpGlliaalsfGhlpavfvpaGpmasGlenkekakvrqlfaeGkvdreell 207
                                               lsh+mfd+a++lGvcdkivpGlli+al+fGhlp+vfvpaGpm+ G++nk+ka+vr+ +a G ++reell
  lcl|NCBI__GCF_001431535.1:WP_057508152.1 142 LSHDMFDAAIYLGVCDKIVPGLLIGALAFGHLPSVFVPAGPMTPGIPNKQKAEVRERYAAGEATREELL 210
                                               ********************************************************************* PP

                                 TIGR01196 208 ksemasyhapGtctfyGtansnqmlvelmGlhlpgasfvnpntplrdaltreaakrlarltakngevlp 276
                                               ++e+asyh++GtctfyGtansnq+l+e mG++lpgasfvnp++ lr altrea+ r+ ++ta ++++ p
  lcl|NCBI__GCF_001431535.1:WP_057508152.1 211 EAEAASYHGAGTCTFYGTANSNQVLLEAMGVQLPGASFVNPEQTLRGALTREATVRALEMTALGDDYRP 279
                                               ********************************************************************* PP

                                 TIGR01196 277 laelideksivnalvgllatGGstnhtlhlvaiaraaGiilnwddlselsdlvpllarvypnGkadvnh 345
                                               ++++ide++ivna+v+l+atGGstnht+h +a+araaGi+++wdd+++ls+l+pll+rvypnG+advn 
  lcl|NCBI__GCF_001431535.1:WP_057508152.1 280 IGRIIDERAIVNAIVALMATGGSTNHTIHWIAVARAAGIVVTWDDMDQLSQLIPLLTRVYPNGEADVNR 348
                                               ********************************************************************* PP

                                 TIGR01196 346 feaaGGlsflirellkeGllhedvetvagkGlrrytkepfledgkleyreaaeksldedilrkvdkpfs 414
                                               f aaGG +f+  el+++Gl+h d+ tva  G+  y++ep l+dg++++ +++ +s+ded+ r vd+pf+
  lcl|NCBI__GCF_001431535.1:WP_057508152.1 349 FAAAGGPAFVFGELIRAGLMHGDIVTVARGGMADYAREPRLQDGQVTWVDGIIRSADEDVARGVDNPFE 417
                                               ********************************************************************* PP

                                 TIGR01196 415 aeGGlkllkGnlGravikvsavkeesrvieapaivfkdqaellaafkagelerdlvavvrfqGpkanGm 483
                                               ++GGl+ll+GnlGr++ik+savk++ r ieapa+v +  + l++   ag l +d+vavvr+qGp+anGm
  lcl|NCBI__GCF_001431535.1:WP_057508152.1 418 SQGGLRLLRGNLGRSLIKLSAVKPQYRSIEAPAVVVDAPQVLNKLHAAGLLPQDFVAVVRYQGPRANGM 486
                                               ********************************************************************* PP

                                 TIGR01196 484 pelhklttvlGvlqdrgfkvalvtdGrlsGasGkvpaaihvtpealegGalakirdGdlirldavngel 552
                                               pelh l + lG+lq++g +valvtdGrlsGasGk+paaih+tpea+ gG+l k+r+Gd+irld+ +g l
  lcl|NCBI__GCF_001431535.1:WP_057508152.1 487 PELHSLAPLLGLLQNQGRRVALVTDGRLSGASGKIPAAIHMTPEAARGGPLGKLREGDIIRLDGEAGTL 555
                                               ********************************************************************* PP

                                 TIGR01196 553 evlvddaelkareleeldlednelGlGrelfaalrekvssaeeGassl 600
                                               evlvd+ae++ar+ + ++   +   lGr+lfa  r  v+ a++Ga+s+
  lcl|NCBI__GCF_001431535.1:WP_057508152.1 556 EVLVDEAEWAART-HAPNTAPAANDLGRNLFAVNRLVVGPADQGAISI 602
                                               ************9.88898889999********************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (601 nodes)
Target sequences:                          1  (638 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 0.02s 00:00:00.05 Elapsed: 00:00:00.04
# Mc/sec: 8.37
//
[ok]

This GapMind analysis is from Sep 24 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