Align phosphogluconate dehydratase (EC 4.2.1.12) (characterized)
to candidate AO353_03420 AO353_03420 phosphogluconate dehydratase
Query= BRENDA::Q1PAG1
(608 letters)
>FitnessBrowser__pseudo3_N2E3:AO353_03420
Length = 608
Score = 1122 bits (2902), Expect = 0.0
Identities = 565/608 (92%), Positives = 584/608 (96%)
Query: 1 MHPRVLEVTERLVARSRATREAYLALIRGAASDGPQRGKLQCANFAHGVAGCGSEDKHSL 60
MHPRVLEVTERLV RSRATREAYLALIRGAASDGP RGKLQCANFAHGVAGCG+EDK SL
Sbjct: 1 MHPRVLEVTERLVTRSRATREAYLALIRGAASDGPMRGKLQCANFAHGVAGCGTEDKQSL 60
Query: 61 RMMNAANVAIVSSYNDMLSAHQPYEHFPEQIKKALREMGSVGQFAGGTPAMCDGVTQGEA 120
RMMNAANVAIVSSYNDMLSAHQPYEH+PEQIK ALRE+GSVGQFAGG PAMCDGVTQGE
Sbjct: 61 RMMNAANVAIVSSYNDMLSAHQPYEHYPEQIKHALREIGSVGQFAGGVPAMCDGVTQGEP 120
Query: 121 GMELSLPSREVIALSTAVALSHNMFDAALMLGICDKIVPGLMMGALRFGHLPTIFVPGGP 180
GMEL + SREVIA+STAVALSHNMFDAA+MLGICDKIVPGLMMGALRFGHLPTIFVPGGP
Sbjct: 121 GMELGIASREVIAMSTAVALSHNMFDAAMMLGICDKIVPGLMMGALRFGHLPTIFVPGGP 180
Query: 181 MPSGISNKEKADVRQRYAEGKATREELLESEMKSYHSPGTCTFYGTANTNQLLMEVMGLH 240
M SGISNKEKADVRQRYAEGKA+REELLESEMKSYHSPGTCTFYGTANTNQLLMEVMGLH
Sbjct: 181 MVSGISNKEKADVRQRYAEGKASREELLESEMKSYHSPGTCTFYGTANTNQLLMEVMGLH 240
Query: 241 LPGASFVNPYTPLRDALTHEAAQQVTRLTKQSGNFTPIGEIVDERSLVNSIVALHATGGS 300
LPGASFVNP TPLRDALT EAA Q+TRLTKQSGNF PIGEIVDERSLVNSIVALHATGGS
Sbjct: 241 LPGASFVNPNTPLRDALTREAAHQITRLTKQSGNFMPIGEIVDERSLVNSIVALHATGGS 300
Query: 301 TNHTLHMPAIAQAAGIQLTWQDMADLSEVVPTLSHVYPNGKADINHFQAAGGMAFLIREL 360
TNHTLHMPAIA AAGIQLTWQDMADLSEVVPTLSHVYPNGKADINHFQAAGGM+FLIREL
Sbjct: 301 TNHTLHMPAIAMAAGIQLTWQDMADLSEVVPTLSHVYPNGKADINHFQAAGGMSFLIREL 360
Query: 361 LEAGLLHEDVNTVAGRGLSRYTQEPFLDNGKLVWRDGPIESLDENILRPVARAFSPEGGL 420
LEAGLLHEDVNTVAG GLSRYTQEPFL+NG+LVWR+GPIESLDENILRPVARAFSPEGGL
Sbjct: 361 LEAGLLHEDVNTVAGHGLSRYTQEPFLENGELVWREGPIESLDENILRPVARAFSPEGGL 420
Query: 421 RVMEGNLGRGVMKVSAVALQHQIVEAPAVVFQDQQDLADAFKAGELEKDFVAVMRFQGPR 480
RVMEGNLGRGVMKVSAVA +HQ+VEAPA+VFQDQQDLADAFKAG LEKDFVAVMRFQGPR
Sbjct: 421 RVMEGNLGRGVMKVSAVAPEHQVVEAPAMVFQDQQDLADAFKAGLLEKDFVAVMRFQGPR 480
Query: 481 SNGMPELHKMTPFLGVLQDRGFKVALVTDGRMSGASGKIPAAIHVSPEAQVGGALARVRD 540
SNGMPELHKMTPFLGVLQDRGFKVALVTDGRMSGASGKIPAAIHVSPEA VGGALARV++
Sbjct: 481 SNGMPELHKMTPFLGVLQDRGFKVALVTDGRMSGASGKIPAAIHVSPEAFVGGALARVQE 540
Query: 541 GDIIRVDGVKGTLELKVDADEFAAREPAKGLLGNNVGSGRELFGFMRMAFSSAEQGASAF 600
GDIIRVDGVKGTL+L VDADEFAAR PAKGLL N +G GRELFGFMRMAFSSAEQGASAF
Sbjct: 541 GDIIRVDGVKGTLQLLVDADEFAARTPAKGLLDNGIGCGRELFGFMRMAFSSAEQGASAF 600
Query: 601 TSALENLK 608
TSALE LK
Sbjct: 601 TSALETLK 608
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: 1351
Number of extensions: 49
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 AO353_03420 AO353_03420 (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.4737.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
------- ------ ----- ------- ------ ----- ---- -- -------- -----------
0 1040.1 0.8 0 1039.9 0.8 1.0 1 lcl|FitnessBrowser__pseudo3_N2E3:AO353_03420 AO353_03420 phosphogluconate deh
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo3_N2E3:AO353_03420 AO353_03420 phosphogluconate dehydratase
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1039.9 0.8 0 0 1 601 [] 2 601 .. 2 601 .. 0.99
Alignments for each domain:
== domain 1 score: 1039.9 bits; conditional E-value: 0
TIGR01196 1 hsrlaeiteriierskktrekylekirsaktkgklrstlgcgnlahgvaalsesekvelksekrk 65
h+r++e+ter++ rs++tre+yl+ ir a++ g++r++l c+n+ahgva + ++k++l+ ++ +
lcl|FitnessBrowser__pseudo3_N2E3:AO353_03420 2 HPRVLEVTERLVTRSRATREAYLALIRGAASDGPMRGKLQCANFAHGVAGCGTEDKQSLRMMNAA 66
79*************************************************************** PP
TIGR01196 66 nlaiitayndmlsahqpfkeypdlikkalqeanavaqvagGvpamcdGvtqGedGmelsllsrdv 130
n+ai+++yndmlsahqp+++yp++ik+al+e ++v+q agGvpamcdGvtqGe+Gmel ++sr+v
lcl|FitnessBrowser__pseudo3_N2E3:AO353_03420 67 NVAIVSSYNDMLSAHQPYEHYPEQIKHALREIGSVGQFAGGVPAMCDGVTQGEPGMELGIASREV 131
***************************************************************** PP
TIGR01196 131 ialstaiglshnmfdgalflGvcdkivpGlliaalsfGhlpavfvpaGpmasGlenkekakvrql 195
ia+sta++lshnmfd+a++lG+cdkivpGl+++al fGhlp++fvp+Gpm+sG++nkeka vrq
lcl|FitnessBrowser__pseudo3_N2E3:AO353_03420 132 IAMSTAVALSHNMFDAAMMLGICDKIVPGLMMGALRFGHLPTIFVPGGPMVSGISNKEKADVRQR 196
***************************************************************** PP
TIGR01196 196 faeGkvdreellksemasyhapGtctfyGtansnqmlvelmGlhlpgasfvnpntplrdaltrea 260
+aeGk++reell+sem+syh+pGtctfyGtan+nq+l+e+mGlhlpgasfvnpntplrdaltrea
lcl|FitnessBrowser__pseudo3_N2E3:AO353_03420 197 YAEGKASREELLESEMKSYHSPGTCTFYGTANTNQLLMEVMGLHLPGASFVNPNTPLRDALTREA 261
***************************************************************** PP
TIGR01196 261 akrlarltakngevlplaelideksivnalvgllatGGstnhtlhlvaiaraaGiilnwddlsel 325
a++++rlt ++g+++p++e++de+s+vn++v+l+atGGstnhtlh+ aia aaGi+l+w+d+ +l
lcl|FitnessBrowser__pseudo3_N2E3:AO353_03420 262 AHQITRLTKQSGNFMPIGEIVDERSLVNSIVALHATGGSTNHTLHMPAIAMAAGIQLTWQDMADL 326
***************************************************************** PP
TIGR01196 326 sdlvpllarvypnGkadvnhfeaaGGlsflirellkeGllhedvetvagkGlrrytkepfledgk 390
s++vp+l +vypnGkad+nhf+aaGG+sflirell++Gllhedv+tvag+Gl+ryt+epfle+g+
lcl|FitnessBrowser__pseudo3_N2E3:AO353_03420 327 SEVVPTLSHVYPNGKADINHFQAAGGMSFLIRELLEAGLLHEDVNTVAGHGLSRYTQEPFLENGE 391
***************************************************************** PP
TIGR01196 391 leyreaaeksldedilrkvdkpfsaeGGlkllkGnlGravikvsavkeesrvieapaivfkdqae 455
l++re++ +slde+ilr+v + fs+eGGl++++GnlGr+v+kvsav++e++v+eapa+vf+dq++
lcl|FitnessBrowser__pseudo3_N2E3:AO353_03420 392 LVWREGPIESLDENILRPVARAFSPEGGLRVMEGNLGRGVMKVSAVAPEHQVVEAPAMVFQDQQD 456
***************************************************************** PP
TIGR01196 456 llaafkagelerdlvavvrfqGpkanGmpelhklttvlGvlqdrgfkvalvtdGrlsGasGkvpa 520
l++afkag le+d+vav+rfqGp++nGmpelhk+t++lGvlqdrgfkvalvtdGr+sGasGk+pa
lcl|FitnessBrowser__pseudo3_N2E3:AO353_03420 457 LADAFKAGLLEKDFVAVMRFQGPRSNGMPELHKMTPFLGVLQDRGFKVALVTDGRMSGASGKIPA 521
***************************************************************** PP
TIGR01196 521 aihvtpealegGalakirdGdlirldavngelevlvddaelkareleeldlednelGlGrelfaa 585
aihv+pea gGala++++Gd+ir+d+v+g l++lvd e++ar++++ l dn +G+Grelf +
lcl|FitnessBrowser__pseudo3_N2E3:AO353_03420 522 AIHVSPEAFVGGALARVQEGDIIRVDGVKGTLQLLVDADEFAARTPAK-GLLDNGIGCGRELFGF 585
*********************************************765.688999********** PP
TIGR01196 586 lrekvssaeeGasslt 601
+r + ssae+Gas++t
lcl|FitnessBrowser__pseudo3_N2E3:AO353_03420 586 MRMAFSSAEQGASAFT 601
************9986 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: 0.04u 0.02s 00:00:00.06 Elapsed: 00:00:00.04
# Mc/sec: 7.68
//
[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