Align Phosphogluconate dehydratase; 6-phosphogluconate dehydratase; EC 4.2.1.12 (characterized)
to candidate Ac3H11_2082 Phosphogluconate dehydratase (EC 4.2.1.12)
Query= SwissProt::P21909
(607 letters)
>lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2082 Phosphogluconate
dehydratase (EC 4.2.1.12)
Length = 589
Score = 661 bits (1706), Expect = 0.0
Identities = 331/598 (55%), Positives = 436/598 (72%), Gaps = 16/598 (2%)
Query: 4 LHSTVEKVTARVIERSRETRKAYLDLIQYEREKGVDRPNLSCSNLAHGFAAMNG-DKPAL 62
+H V +VT R+++RS +TR AYL + + + + C+NLAH +AA+ G +K +
Sbjct: 1 MHPVVARVTERIVQRSADTRGAYLAGVDAMIARKPAQDRMGCANLAHAYAALPGSEKFKV 60
Query: 63 RDFNRMNIGVVTSYNDMLSAHEPYYRYPEQMKVFAREVGATVQVAGGVPAMCDGVTQGQP 122
NIGVVT+YNDMLSAH+PY YP ++ A + GATVQVAGGVPAMCDGVTQG P
Sbjct: 61 TVEKAPNIGVVTAYNDMLSAHQPYQSYPAVLRDEAAKQGATVQVAGGVPAMCDGVTQGTP 120
Query: 123 GMEESLFSRDVIALATSVSLSHGMFEGAALLGICDKIVPGLLMGALRFGHLPTILVPSGP 182
GME SLFSRD IA+AT+V+LSH +F+GA LLG+CDKIVPGLL+GAL +GHLP + VP+GP
Sbjct: 121 GMELSLFSRDAIAMATAVALSHDVFDGALLLGVCDKIVPGLLIGALHYGHLPCVFVPAGP 180
Query: 183 MTTGIPNKEKIRIRQLYAQGKIGQKELLDMEAACYHAEGTCTFYGTANTNQMVMEVLGLH 242
M TG+ NK+K ++R+ YAQG +G+ ELL E+A YH+ GTCTFYGTAN+NQM++E +GLH
Sbjct: 181 MGTGLSNKDKAKVREQYAQGLVGRDELLQAESAAYHSPGTCTFYGTANSNQMLLEAMGLH 240
Query: 243 MPGSAFVTPGTPLRQALTRAAVHRVAELGWKGDDYRPLGKIIDEKSIVNAIVGLLATGGS 302
+PG+AF +PGT R+A TR A+ V ++G + + P+GK++DE+ IVNA+ LLATGGS
Sbjct: 241 VPGAAFESPGTEAREAFTRQALRTVLDIGKRSKRFTPIGKLVDERCIVNAMAALLATGGS 300
Query: 303 TNHTMHIPAIARAAGVIVNWNDFHDLSEVVPLIARIYPNGPRDINEFQNAGGMAYVIKEL 362
TNH +H AIAR+AG++++W DF +LS VVPL+AR+YPNG D+N+FQ AGG ++++EL
Sbjct: 301 TNHLIHWVAIARSAGILIDWTDFDELSSVVPLLARVYPNGDADVNQFQAAGGPPWILREL 360
Query: 363 LSANLLNRDVTTIAKGGIEEYAK-APALNDAGELVWKPAGEPGDDTILRPVSNPFAKDGG 421
L+ ++ DV ++ GGI + K APA++ GD ++LRPVS PF+ GG
Sbjct: 361 LAGGFMHPDVMSVNVGGIADGGKSAPAVS-------------GDTSVLRPVSAPFSPTGG 407
Query: 422 LRLLEGNLGRAMYKASAVDPKFWTIEAPVRVFSDQDDVQKAFKAGELNKDVIVVVRFQGP 481
LRLL+G LGRA+ K SAV IEAP RVF Q+ + AF AG++N+D++ VVRFQGP
Sbjct: 408 LRLLQGRLGRAVIKVSAVPEDRHIIEAPARVFDSQEALLAAFSAGDVNQDMVAVVRFQGP 467
Query: 482 RANGMPELHKLTPALGVLQDNGYKVALVTDGRMSGATGKVPVALHVSPEALGGGAIGKLR 541
+ANGMPELHKLTP L VLQ+ G+KVALVTDGRMSGA+GKVP A+HV+PEAL GG + K+R
Sbjct: 468 QANGMPELHKLTPPLAVLQNQGFKVALVTDGRMSGASGKVPAAIHVTPEALAGGPLAKVR 527
Query: 542 DGDIVRISVEEGKLEALVPADEWNAR-PHAEKPAFRPGTGRELFDIFRQNAAKAEDGA 598
DGDIVR+ G L+ LV W AR P + G GRELF FR++A AE GA
Sbjct: 528 DGDIVRVDAVAGTLDVLVDEATWAARTPSPYSAPAQTGFGRELFTNFRRHAGGAEQGA 585
Lambda K H
0.318 0.136 0.403
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: 1114
Number of extensions: 48
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: 607
Length of database: 589
Length adjustment: 37
Effective length of query: 570
Effective length of database: 552
Effective search space: 314640
Effective search space used: 314640
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 Ac3H11_2082 (Phosphogluconate dehydratase (EC 4.2.1.12))
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.13440.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
------- ------ ----- ------- ------ ----- ---- -- -------- -----------
4.5e-270 882.9 0.2 8.7e-270 882.0 0.2 1.4 1 lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2082 Phosphogluconate dehydratase (EC
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2082 Phosphogluconate dehydratase (EC 4.2.1.12)
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 882.0 0.2 8.7e-270 8.7e-270 1 599 [. 2 587 .. 2 589 .] 0.98
Alignments for each domain:
== domain 1 score: 882.0 bits; conditional E-value: 8.7e-270
TIGR01196 1 hsrlaeiteriierskktrekylekirsaktkgklrstlgcgnlahgvaalsesekvelkse 62
h+ +a++teri++rs++tr +yl+ + + + + + ++gc+nlah++aal+ sek +++ e
lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2082 2 HPVVARVTERIVQRSADTRGAYLAGVDAMIARKPAQDRMGCANLAHAYAALPGSEKFKVTVE 63
67799********************************************************* PP
TIGR01196 63 krknlaiitayndmlsahqpfkeypdlikkalqeanavaqvagGvpamcdGvtqGedGmels 124
k +n++++tayndmlsahqp+++yp+++++++ +++a+ qvagGvpamcdGvtqG +Gmels
lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2082 64 KAPNIGVVTAYNDMLSAHQPYQSYPAVLRDEAAKQGATVQVAGGVPAMCDGVTQGTPGMELS 125
************************************************************** PP
TIGR01196 125 llsrdvialstaiglshnmfdgalflGvcdkivpGlliaalsfGhlpavfvpaGpmasGlen 186
l+srd ia++ta++lsh++fdgal+lGvcdkivpGlli+al +Ghlp+vfvpaGpm +Gl+n
lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2082 126 LFSRDAIAMATAVALSHDVFDGALLLGVCDKIVPGLLIGALHYGHLPCVFVPAGPMGTGLSN 187
************************************************************** PP
TIGR01196 187 kekakvrqlfaeGkvdreellksemasyhapGtctfyGtansnqmlvelmGlhlpgasfvnp 248
k+kakvr+++a+G v+r+ell++e+a+yh+pGtctfyGtansnqml+e mGlh+pga+f p
lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2082 188 KDKAKVREQYAQGLVGRDELLQAESAAYHSPGTCTFYGTANSNQMLLEAMGLHVPGAAFESP 249
************************************************************** PP
TIGR01196 249 ntplrdaltreaakrlarltakngevlplaelideksivnalvgllatGGstnhtlhlvaia 310
t+ r+a+tr+a + + + ++ +++p+++l+de++ivna+ +llatGGstnh +h vaia
lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2082 250 GTEAREAFTRQALRTVLDIGKRSKRFTPIGKLVDERCIVNAMAALLATGGSTNHLIHWVAIA 311
************************************************************** PP
TIGR01196 311 raaGiilnwddlselsdlvpllarvypnGkadvnhfeaaGGlsflirellkeGllhedvetv 372
r+aGi+++w d++els++vpllarvypnG advn+f+aaGG + ++rell G++h dv +v
lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2082 312 RSAGILIDWTDFDELSSVVPLLARVYPNGDADVNQFQAAGGPPWILRELLAGGFMHPDVMSV 373
************************************************************** PP
TIGR01196 373 agkGlrrytkepfledgkleyreaaeksldedilrkvdkpfsaeGGlkllkGnlGravikvs 434
G+ + a+ s d+++lr+v+ pfs++GGl+ll+G lGravikvs
lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2082 374 NVGGIADG------------GKSAPAVSGDTSVLRPVSAPFSPTGGLRLLQGRLGRAVIKVS 423
99998653............36899************************************* PP
TIGR01196 435 avkeesrvieapaivfkdqaellaafkagelerdlvavvrfqGpkanGmpelhklttvlGvl 496
av e+ ++ieapa+vf++q+ llaaf ag++++d+vavvrfqGp+anGmpelhklt++l vl
lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2082 424 AVPEDRHIIEAPARVFDSQEALLAAFSAGDVNQDMVAVVRFQGPQANGMPELHKLTPPLAVL 485
************************************************************** PP
TIGR01196 497 qdrgfkvalvtdGrlsGasGkvpaaihvtpealegGalakirdGdlirldavngelevlvdd 558
q++gfkvalvtdGr+sGasGkvpaaihvtpeal+gG+lak+rdGd++r+dav+g l+vlvd+
lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2082 486 QNQGFKVALVTDGRMSGASGKVPAAIHVTPEALAGGPLAKVRDGDIVRVDAVAGTLDVLVDE 547
************************************************************** PP
TIGR01196 559 aelkareleeldlednelGlGrelfaalrekvssaeeGass 599
a ++ar+++ + ++ G Grelf+++r+++++ae+Ga++
lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2082 548 ATWAARTPS-PYSAPAQTGFGRELFTNFRRHAGGAEQGACT 587
*******65.55667899*********************96 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (601 nodes)
Target sequences: 1 (589 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: 0.10u 0.01s 00:00:00.11 Elapsed: 00:00:00.10
# Mc/sec: 3.29
//
[ok]
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
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:
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 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