Alignments for a candidate for edd in Thiothrix lacustris DSM 21227

GapMind for catabolism of small carbon sources

Alignments for a candidate for edd in Thiothrix lacustris DSM 21227

Align phosphogluconate dehydratase (EC 4.2.1.12) (characterized)
to candidate WP_028488076.1 Q394_RS0103620 phosphogluconate dehydratase

Query= BRENDA::Q1PAG1
         (608 letters)



>NCBI__GCF_000621325.1:WP_028488076.1
          Length = 611

 Score =  676 bits (1743), Expect = 0.0
 Identities = 353/607 (58%), Positives = 438/607 (72%), Gaps = 5/607 (0%)

Query: 1   MHPRVLEVTERLVARSRATREAYLALIRGAASDGPQRGKLQCANFAHGVAGCGSEDKHSL 60
           +HP+++ VT+R+ ARS A+R AY+  +  A    P R KL C N AH VA   + DK  L
Sbjct: 6   LHPQLVAVTQRIEARSAASRAAYMQQVVAANPVTP-RSKLSCGNLAHAVAAAPNADKLKL 64

Query: 61  RMMNAANVAIVSSYNDMLSAHQPYEHFPEQIKKALREMGSVGQFAGGTPAMCDGVTQGEA 120
               A N+ IV++YNDMLSAHQP+ ++P+ IK A+RE+    Q AGG PAMCDGVTQG+ 
Sbjct: 65  VEWTAGNLGIVTAYNDMLSAHQPFVYYPDLIKAAVREVSGTAQVAGGVPAMCDGVTQGQE 124

Query: 121 GMELSLPSREVIALSTAVALSHNMFDAALMLGICDKIVPGLMMGALRFGHLPTIFVPGGP 180
           GMELSL SR+VIA+S AVALSHN+FDAA  LG+CDKIVPGL++ A  FGHLP IF+P GP
Sbjct: 125 GMELSLFSRDVIAMSAAVALSHNVFDAAAFLGVCDKIVPGLVIAAASFGHLPCIFLPAGP 184

Query: 181 MPSGISNKEKADVRQRYAEGKATREELLESEMKSYHSPGTCTFYGTANTNQLLMEVMGLH 240
           M SG++N  K+ VRQ+YAEGK  R ELL++EM+SYH  GTCTFYGTAN+NQ+LME MGL 
Sbjct: 185 MVSGLANDVKSKVRQQYAEGKVGRAELLQAEMQSYHGAGTCTFYGTANSNQMLMEFMGLQ 244

Query: 241 LPGASFVNPYTPLRDALTHEAAQQVTRLTKQSGNFTPIGEIVDERSLVNSIVALHATGGS 300
           LPG+SFVNP T LR+ALT   AQ+   +T +  ++TP   I+   + VN IV L+ATGGS
Sbjct: 245 LPGSSFVNPGTSLREALTVAGAQRALAMTAKGQDYTPAANILTVNAFVNGIVGLNATGGS 304

Query: 301 TNHTLHMPAIAQAAGIQLTWQDMADLSEVVPTLSHVYPNGKADINHFQAAGGMAFLIREL 360
           TN  LH+ A+A+AAGI L  +D ADLS + P ++ VYPNG AD+NHF AAGG+ F+IREL
Sbjct: 305 TNLLLHLVAMARAAGIVLCLEDFADLSAITPLIARVYPNGVADVNHFHAAGGLQFVIREL 364

Query: 361 LEAGLLHEDVNTVAGRGLSRYTQEPFL-DNGKLVWRDGPIESLDENILRPVARAFSPEGG 419
           L AGLLHE+V+TVAG+GL  YTQE  L  +G + WR+G   S D ++LRPV + F P GG
Sbjct: 365 LAAGLLHEEVDTVAGKGLHHYTQEAVLAADGTVTWREGASTSHDTDVLRPVVQPFQPSGG 424

Query: 420 LRVMEGNLGRGVMKVSAVALQHQIVEAPAVVFQDQQDLADAFKAGELEKDFVAVMRFQGP 479
           L  + GNLG  V+KVSAV     ++EAPA VF DQ  +  AF+AGELE DFV V+RFQGP
Sbjct: 425 LVRLLGNLGDSVIKVSAVKPDKHLIEAPAKVFHDQAAVKAAFEAGELEGDFVCVVRFQGP 484

Query: 480 RSNGMPELHKMTPFLGVLQDRGFKVALVTDGRMSGASGKIPAAIHVSPEAQVGGALARVR 539
           ++NGMPELH +TP LG+LQDRG  VALVTDGRMSGASGK+PAAIHVSPEA  GGA+A++R
Sbjct: 485 KANGMPELHGLTPVLGLLQDRGQHVALVTDGRMSGASGKVPAAIHVSPEAMDGGAIAKIR 544

Query: 540 DGDIIRVDGVKGTLELKVDADEFAAREPAK-GLLGNNVGSGRELFGFMRMAFSSAEQGAS 598
           DGD+IR+D   G LE+      FA R P    L  N  G GRELF   R   S+A  GAS
Sbjct: 545 DGDLIRLDVDNGHLEVLTAG--FAERAPVSVDLSANGSGCGRELFQVFRSHVSAAASGAS 602

Query: 599 AFTSALE 605
           A  +  E
Sbjct: 603 ALFTDTE 609


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: 1064
Number of extensions: 45
Number of successful extensions: 4
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: 611
Length adjustment: 37
Effective length of query: 571
Effective length of database: 574
Effective search space:   327754
Effective search space used:   327754
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 WP_028488076.1 Q394_RS0103620 (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.1951530.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.9e-289  946.9   5.8   2.3e-289  946.7   5.8    1.0  1  NCBI__GCF_000621325.1:WP_028488076.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000621325.1:WP_028488076.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  946.7   5.8  2.3e-289  2.3e-289       1     600 [.       7     604 ..       7     605 .. 0.98

  Alignments for each domain:
  == domain 1  score: 946.7 bits;  conditional E-value: 2.3e-289
                             TIGR01196   1 hsrlaeiteriierskktrekylekirsaktkgklrstlgcgnlahgvaalsesekvelksekrknlaiitay 73 
                                           h++l+++t+ri +rs++ r +y++++ +a+  ++ rs+l+cgnlah+vaa ++++k++l + +  nl+i+tay
  NCBI__GCF_000621325.1:WP_028488076.1   7 HPQLVAVTQRIEARSAASRAAYMQQVVAANPVTP-RSKLSCGNLAHAVAAAPNADKLKLVEWTAGNLGIVTAY 78 
                                           799***********************98877766.677*********************************** PP

                             TIGR01196  74 ndmlsahqpfkeypdlikkalqeanavaqvagGvpamcdGvtqGedGmelsllsrdvialstaiglshnmfdg 146
                                           ndmlsahqpf  ypdlik a++e +++aqvagGvpamcdGvtqG++Gmelsl+srdvia+s+a++lshn+fd+
  NCBI__GCF_000621325.1:WP_028488076.1  79 NDMLSAHQPFVYYPDLIKAAVREVSGTAQVAGGVPAMCDGVTQGQEGMELSLFSRDVIAMSAAVALSHNVFDA 151
                                           ************************************************************************* PP

                             TIGR01196 147 alflGvcdkivpGlliaalsfGhlpavfvpaGpmasGlenkekakvrqlfaeGkvdreellksemasyhapGt 219
                                           a flGvcdkivpGl+iaa+sfGhlp++f+paGpm+sGl n+ k+kvrq++aeGkv+r ell++em+syh++Gt
  NCBI__GCF_000621325.1:WP_028488076.1 152 AAFLGVCDKIVPGLVIAAASFGHLPCIFLPAGPMVSGLANDVKSKVRQQYAEGKVGRAELLQAEMQSYHGAGT 224
                                           ************************************************************************* PP

                             TIGR01196 220 ctfyGtansnqmlvelmGlhlpgasfvnpntplrdaltreaakrlarltakngevlplaelideksivnalvg 292
                                           ctfyGtansnqml+e+mGl+lpg+sfvnp t lr+alt + a+r+ ++tak+++++p+a++++ +++vn++vg
  NCBI__GCF_000621325.1:WP_028488076.1 225 CTFYGTANSNQMLMEFMGLQLPGSSFVNPGTSLREALTVAGAQRALAMTAKGQDYTPAANILTVNAFVNGIVG 297
                                           ************************************************************************* PP

                             TIGR01196 293 llatGGstnhtlhlvaiaraaGiilnwddlselsdlvpllarvypnGkadvnhfeaaGGlsflirellkeGll 365
                                           l atGGstn  lhlva+araaGi+l  +d+ +ls + pl+arvypnG advnhf+aaGGl+f+irell +Gll
  NCBI__GCF_000621325.1:WP_028488076.1 298 LNATGGSTNLLLHLVAMARAAGIVLCLEDFADLSAITPLIARVYPNGVADVNHFHAAGGLQFVIRELLAAGLL 370
                                           ************************************************************************* PP

                             TIGR01196 366 hedvetvagkGlrrytkepfle.dgkleyreaaeksldedilrkvdkpfsaeGGlkllkGnlGravikvsavk 437
                                           he+v+tvagkGl++yt+e++l  dg +++re+a +s d+d+lr+v +pf+++GGl  l GnlG +vikvsavk
  NCBI__GCF_000621325.1:WP_028488076.1 371 HEEVDTVAGKGLHHYTQEAVLAaDGTVTWREGASTSHDTDVLRPVVQPFQPSGGLVRLLGNLGDSVIKVSAVK 443
                                           ******************999636************************************************* PP

                             TIGR01196 438 eesrvieapaivfkdqaellaafkagelerdlvavvrfqGpkanGmpelhklttvlGvlqdrgfkvalvtdGr 510
                                           ++++ ieapa+vf+dqa ++aaf+agele+d+v+vvrfqGpkanGmpelh lt+vlG+lqdrg+ valvtdGr
  NCBI__GCF_000621325.1:WP_028488076.1 444 PDKHLIEAPAKVFHDQAAVKAAFEAGELEGDFVCVVRFQGPKANGMPELHGLTPVLGLLQDRGQHVALVTDGR 516
                                           ************************************************************************* PP

                             TIGR01196 511 lsGasGkvpaaihvtpealegGalakirdGdlirldavngelevlvddaelkareleeldlednelGlGrelf 583
                                           +sGasGkvpaaihv+pea++gGa+akirdGdlirld  ng+levl   +  + r + ++dl++n  G+Grelf
  NCBI__GCF_000621325.1:WP_028488076.1 517 MSGASGKVPAAIHVSPEAMDGGAIAKIRDGDLIRLDVDNGHLEVLTAGF--AERAPVSVDLSANGSGCGRELF 587
                                           *********************************************9765..677788**************** PP

                             TIGR01196 584 aalrekvssaeeGassl 600
                                             +r++vs+a +Gas+l
  NCBI__GCF_000621325.1:WP_028488076.1 588 QVFRSHVSAAASGASAL 604
                                           **************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (601 nodes)
Target sequences:                          1  (611 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 31.28
//
[ok]

This GapMind analysis is from Apr 09 2024. 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:

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 2024 update 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