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)
>FitnessBrowser__acidovorax_3H11:Ac3H11_2082
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.25699.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: 3.32
//
[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:
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