Align phosphogluconate dehydratase (EC 4.2.1.12) (characterized)
to candidate PfGW456L13_1889 Phosphogluconate dehydratase (EC 4.2.1.12)
Query= BRENDA::Q1PAG1
(608 letters)
>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1889
Length = 608
Score = 1114 bits (2881), Expect = 0.0
Identities = 561/607 (92%), Positives = 586/607 (96%)
Query: 1 MHPRVLEVTERLVARSRATREAYLALIRGAASDGPQRGKLQCANFAHGVAGCGSEDKHSL 60
MHPRVLEVTERL+ARSRATREAYLALIRGAASDGP RGKLQCANFAHGVAGCGS+DKHSL
Sbjct: 1 MHPRVLEVTERLIARSRATREAYLALIRGAASDGPMRGKLQCANFAHGVAGCGSDDKHSL 60
Query: 61 RMMNAANVAIVSSYNDMLSAHQPYEHFPEQIKKALREMGSVGQFAGGTPAMCDGVTQGEA 120
RMMN+AN+AIVSSYNDMLSAHQPYE FPE IKKALRE+GSVGQFAGGTPAMCDGVTQGE
Sbjct: 61 RMMNSANIAIVSSYNDMLSAHQPYEVFPELIKKALREIGSVGQFAGGTPAMCDGVTQGEP 120
Query: 121 GMELSLPSREVIALSTAVALSHNMFDAALMLGICDKIVPGLMMGALRFGHLPTIFVPGGP 180
GMELSLPSREVIALSTAVALSHNMFD AL+LGICDKIVPGLMMGALRFGHLP IFVPGGP
Sbjct: 121 GMELSLPSREVIALSTAVALSHNMFDGALLLGICDKIVPGLMMGALRFGHLPMIFVPGGP 180
Query: 181 MPSGISNKEKADVRQRYAEGKATREELLESEMKSYHSPGTCTFYGTANTNQLLMEVMGLH 240
M SGISNK+KADVRQ+YAEGKATREELLESEMKSYHSPGTCTFYGTANTNQLLMEVMGLH
Sbjct: 181 MVSGISNKQKADVRQKYAEGKATREELLESEMKSYHSPGTCTFYGTANTNQLLMEVMGLH 240
Query: 241 LPGASFVNPYTPLRDALTHEAAQQVTRLTKQSGNFTPIGEIVDERSLVNSIVALHATGGS 300
LPGASFVNP TPLRDALT EAA QVTRLTKQ+G+F PIGEIVDERSLVNSIVALHATGGS
Sbjct: 241 LPGASFVNPNTPLRDALTREAAHQVTRLTKQNGDFMPIGEIVDERSLVNSIVALHATGGS 300
Query: 301 TNHTLHMPAIAQAAGIQLTWQDMADLSEVVPTLSHVYPNGKADINHFQAAGGMAFLIREL 360
TNHTLHMPAIA AAGIQLTWQDMADLSEVVPTLSHVYPNGKADINHFQAAGGM+FLIREL
Sbjct: 301 TNHTLHMPAIAMAAGIQLTWQDMADLSEVVPTLSHVYPNGKADINHFQAAGGMSFLIREL 360
Query: 361 LEAGLLHEDVNTVAGRGLSRYTQEPFLDNGKLVWRDGPIESLDENILRPVARAFSPEGGL 420
LEAGLLHE+VNTV G GLSRYTQEPFLDNG+LVWR+G +SLDE+ILRPVARAFS EGGL
Sbjct: 361 LEAGLLHENVNTVMGHGLSRYTQEPFLDNGQLVWREGVTDSLDESILRPVARAFSAEGGL 420
Query: 421 RVMEGNLGRGVMKVSAVALQHQIVEAPAVVFQDQQDLADAFKAGELEKDFVAVMRFQGPR 480
RVMEGNLGRGVMKVSAVA+++QIVEAPA+VFQDQQDLADAFKAG LEKDFVAVMRFQGPR
Sbjct: 421 RVMEGNLGRGVMKVSAVAVENQIVEAPAMVFQDQQDLADAFKAGLLEKDFVAVMRFQGPR 480
Query: 481 SNGMPELHKMTPFLGVLQDRGFKVALVTDGRMSGASGKIPAAIHVSPEAQVGGALARVRD 540
SNGMPELHKMTPFLGVLQDRGFKVALVTDGRMSGASGKIPAAIHVSPEA VGGALARV++
Sbjct: 481 SNGMPELHKMTPFLGVLQDRGFKVALVTDGRMSGASGKIPAAIHVSPEAYVGGALARVQE 540
Query: 541 GDIIRVDGVKGTLELKVDADEFAAREPAKGLLGNNVGSGRELFGFMRMAFSSAEQGASAF 600
GDIIRVDGVKGTLELKVDA+EFAAR PAKGLLGNN+G+GRELFGFMRMAFSSAEQGASAF
Sbjct: 541 GDIIRVDGVKGTLELKVDAEEFAARTPAKGLLGNNIGTGRELFGFMRMAFSSAEQGASAF 600
Query: 601 TSALENL 607
TSALE L
Sbjct: 601 TSALETL 607
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: 1341
Number of extensions: 44
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 PfGW456L13_1889 (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.927.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 1029.7 1.1 0 1029.5 1.1 1.0 1 lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1889 Phosphogluconate dehydratase (EC
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1889 Phosphogluconate dehydratase (EC 4.2.1.12)
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1029.5 1.1 0 0 1 601 [] 2 601 .. 2 601 .. 0.99
Alignments for each domain:
== domain 1 score: 1029.5 bits; conditional E-value: 0
TIGR01196 1 hsrlaeiteriierskktrekylekirsaktkgklrstlgcgnlahgvaalsese 55
h+r++e+ter+i+rs++tre+yl+ ir a++ g++r++l c+n+ahgva + ++
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1889 2 HPRVLEVTERLIARSRATREAYLALIRGAASDGPMRGKLQCANFAHGVAGCGSDD 56
79***************************************************** PP
TIGR01196 56 kvelksekrknlaiitayndmlsahqpfkeypdlikkalqeanavaqvagGvpam 110
k +l+ ++ +n+ai+++yndmlsahqp++ +p+likkal+e ++v+q agG+pam
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1889 57 KHSLRMMNSANIAIVSSYNDMLSAHQPYEVFPELIKKALREIGSVGQFAGGTPAM 111
******************************************************* PP
TIGR01196 111 cdGvtqGedGmelsllsrdvialstaiglshnmfdgalflGvcdkivpGlliaal 165
cdGvtqGe+Gmelsl sr+vialsta++lshnmfdgal+lG+cdkivpGl+++al
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1889 112 CDGVTQGEPGMELSLPSREVIALSTAVALSHNMFDGALLLGICDKIVPGLMMGAL 166
******************************************************* PP
TIGR01196 166 sfGhlpavfvpaGpmasGlenkekakvrqlfaeGkvdreellksemasyhapGtc 220
fGhlp +fvp+Gpm+sG++nk+ka vrq +aeGk++reell+sem+syh+pGtc
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1889 167 RFGHLPMIFVPGGPMVSGISNKQKADVRQKYAEGKATREELLESEMKSYHSPGTC 221
******************************************************* PP
TIGR01196 221 tfyGtansnqmlvelmGlhlpgasfvnpntplrdaltreaakrlarltakngevl 275
tfyGtan+nq+l+e+mGlhlpgasfvnpntplrdaltreaa++++rlt +ng+++
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1889 222 TFYGTANTNQLLMEVMGLHLPGASFVNPNTPLRDALTREAAHQVTRLTKQNGDFM 276
******************************************************* PP
TIGR01196 276 plaelideksivnalvgllatGGstnhtlhlvaiaraaGiilnwddlselsdlvp 330
p++e++de+s+vn++v+l+atGGstnhtlh+ aia aaGi+l+w+d+ +ls++vp
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1889 277 PIGEIVDERSLVNSIVALHATGGSTNHTLHMPAIAMAAGIQLTWQDMADLSEVVP 331
******************************************************* PP
TIGR01196 331 llarvypnGkadvnhfeaaGGlsflirellkeGllhedvetvagkGlrrytkepf 385
+l +vypnGkad+nhf+aaGG+sflirell++Gllhe+v+tv+g+Gl+ryt+epf
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1889 332 TLSHVYPNGKADINHFQAAGGMSFLIRELLEAGLLHENVNTVMGHGLSRYTQEPF 386
******************************************************* PP
TIGR01196 386 ledgkleyreaaeksldedilrkvdkpfsaeGGlkllkGnlGravikvsavkees 440
l++g+l++re++ slde+ilr+v + fsaeGGl++++GnlGr+v+kvsav+ e+
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1889 387 LDNGQLVWREGVTDSLDESILRPVARAFSAEGGLRVMEGNLGRGVMKVSAVAVEN 441
******************************************************* PP
TIGR01196 441 rvieapaivfkdqaellaafkagelerdlvavvrfqGpkanGmpelhklttvlGv 495
+++eapa+vf+dq++l++afkag le+d+vav+rfqGp++nGmpelhk+t++lGv
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1889 442 QIVEAPAMVFQDQQDLADAFKAGLLEKDFVAVMRFQGPRSNGMPELHKMTPFLGV 496
******************************************************* PP
TIGR01196 496 lqdrgfkvalvtdGrlsGasGkvpaaihvtpealegGalakirdGdlirldavng 550
lqdrgfkvalvtdGr+sGasGk+paaihv+pea+ gGala++++Gd+ir+d+v+g
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1889 497 LQDRGFKVALVTDGRMSGASGKIPAAIHVSPEAYVGGALARVQEGDIIRVDGVKG 551
******************************************************* PP
TIGR01196 551 elevlvddaelkareleeldlednelGlGrelfaalrekvssaeeGasslt 601
le+ vd e++ar++++ l n++G+Grelf ++r + ssae+Gas++t
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1889 552 TLELKVDAEEFAARTPAK-GLLGNNIGTGRELFGFMRMAFSSAEQGASAFT 601
***************776.566789**********************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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 12.50
//
[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