Align Dihydroxy-acid dehydratase, mitochondrial; DAD; 2,3-dihydroxy acid hydrolyase; EC 4.2.1.9 (characterized)
to candidate PfGW456L13_3725 Dihydroxy-acid dehydratase (EC 4.2.1.9)
Query= SwissProt::P39522
(585 letters)
>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3725
Length = 560
Score = 572 bits (1473), Expect = e-167
Identities = 285/562 (50%), Positives = 383/562 (68%), Gaps = 11/562 (1%)
Query: 23 LNKYSYIITEPKGQGASQAMLYATGFKKEDFKKPQVGVGSCWWSGNPCNMHLLDLNNRCS 82
L KYS + + ++AML A GF DF KPQ+G+ S W PCNMH+ L
Sbjct: 7 LRKYSSQVIDGVEAAPARAMLRAVGFTDADFTKPQIGIASTWAMVTPCNMHIDKLALEAE 66
Query: 83 QSIEKAGLKAMQFNTIGVSDGISMGTKGMRYSLQSREIIADSFETIMMAQHYDANIAIPS 142
+ AG K + FNTI +SDGI+ GT+GM+YSL SRE+IADS E + + +D + I
Sbjct: 67 KGANAAGAKGVIFNTITISDGIANGTEGMKYSLVSREVIADSIEVVTGCEGFDGLVTIGG 126
Query: 143 CDKNMPGVMMAMGRHNRPSIMVYGGTILPGHPTCGSSKISKNIDIVSAFQSYGEYISKQF 202
CDKNMPG ++ M R NRPSI VYGGTI PG + + DI+S F++ G++
Sbjct: 127 CDKNMPGCLIGMARLNRPSIFVYGGTIQPG---------AGHTDIISVFEAVGQHARGDI 177
Query: 203 TEEEREDVVEHACPGPGSCGGMYTANTMASAAEVLGLTIPNSSSFPAVSKEKLAECDNIG 262
+E + + + E A PGPGSCGGMYTANTMASA E LG+++P SSS A+ +K ++ G
Sbjct: 178 SEIQVKQIEEVAIPGPGSCGGMYTANTMASAIEALGMSLPGSSSQDAIGADKASDSFRAG 237
Query: 263 EYIKKTMELGILPRDILTKEAFENAITYVVATGGSTNAVLHLVAVAHSAGVKLSPDDFQR 322
+ + + ++L + PRDI+T++AFENAI V+A GSTNAVLHL+A+A++ V+L+ DDF
Sbjct: 238 QQVMELLKLDLKPRDIMTRKAFENAIRVVIALAGSTNAVLHLLAMANAVDVELTLDDFVE 297
Query: 323 ISDTTPLIGDFKPSGKYVMADLINVGGTQSVIKYLYENNMLHGNTMTVTGDTLAERAKKA 382
+ +P++ D +PSGKY+M++L+ +GG Q ++K + + MLHG+ +TVTG TLAE
Sbjct: 298 LGKVSPVVADLRPSGKYMMSELVAIGGIQPLMKRMLDAGMLHGDVLTVTGQTLAENLASV 357
Query: 383 PSLPEGQEIIKPLSHPIKANGHLQILYGSLAPGGAVGKITGKEGTYFKGRARVFEEEGAF 442
P P GQ++I+P PIK + HL IL G+L+P GAV KITGKEG F+G ARV+ E
Sbjct: 358 PDYPAGQDVIRPFDQPIKKDSHLVILRGNLSPTGAVAKITGKEGLRFEGTARVYHGEEGA 417
Query: 443 IEALERGEIKKGEKTVVVIRYEGPRGAPGMPEMLKPSSALMGYGLGKDVALLTDGRFSGG 502
+ + GE++ GE V+VIRYEGP+G PGM EML P+SA+MG GLGK+VAL+TDGRFSGG
Sbjct: 418 LAGILNGEVQPGE--VIVIRYEGPKGGPGMREMLSPTSAVMGKGLGKEVALITDGRFSGG 475
Query: 503 SHGFLIGHIVPEAAEGGPIGLVRDGDEIIIDADNNKIDLLVSDKEMAQRKQSWVAPPPRY 562
SHGF++GHI PEA EGGPI LV +GD IIIDA+ I + VSD +A+RK WV P +Y
Sbjct: 476 SHGFVVGHITPEAFEGGPIALVENGDRIIIDAETRLITVDVSDAVLAERKSRWVRPESKY 535
Query: 563 TRGTLSKYAKLVSNASNGCVLD 584
RG L+KYAK VS+AS G V D
Sbjct: 536 KRGVLAKYAKTVSSASEGAVTD 557
Lambda K H
0.315 0.134 0.390
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: 994
Number of extensions: 45
Number of successful extensions: 3
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: 585
Length of database: 560
Length adjustment: 36
Effective length of query: 549
Effective length of database: 524
Effective search space: 287676
Effective search space used: 287676
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 (21.6 bits)
S2: 53 (25.0 bits)
Align candidate PfGW456L13_3725 (Dihydroxy-acid dehydratase (EC 4.2.1.9))
to HMM TIGR00110 (ilvD: dihydroxy-acid dehydratase (EC 4.2.1.9))
# 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.aa/TIGR00110.hmm
# target sequence database: /tmp/gapView.12745.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: TIGR00110 [M=543]
Accession: TIGR00110
Description: ilvD: dihydroxy-acid 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
------- ------ ----- ------- ------ ----- ---- -- -------- -----------
7.8e-226 736.7 8.1 9e-226 736.5 8.1 1.0 1 lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3725 Dihydroxy-acid dehydratase (EC 4
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3725 Dihydroxy-acid dehydratase (EC 4.2.1.9)
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 736.5 8.1 9e-226 9e-226 1 542 [. 22 557 .. 22 558 .. 0.99
Alignments for each domain:
== domain 1 score: 736.5 bits; conditional E-value: 9e-226
TIGR00110 1 aarallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgva 55
+ara+l+a+G++d+d++kP+i++++++ ++P+++h+++la ++++ +aaG++
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3725 22 PARAMLRAVGFTDADFTKPQIGIASTWAMVTPCNMHIDKLALEAEKGANAAGAKG 76
579**************************************************** PP
TIGR00110 56 kefntiavsDGiamgheGmkysLpsreiiaDsvetvvkahalDalvvissCDkiv 110
+ fnti++sDGia g+eGmkysL+sre+iaDs+e v + +D+lv+i+ CDk++
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3725 77 VIFNTITISDGIANGTEGMKYSLVSREVIADSIEVVTGCEGFDGLVTIGGCDKNM 131
******************************************************* PP
TIGR00110 111 PGmlmaalrlniPaivvsGGpmeagktklsekidlvdvfeavgeyaagklseeel 165
PG l++++rln+P+i+v+GG++++g + d+++vfeavg+ a g++se ++
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3725 132 PGCLIGMARLNRPSIFVYGGTIQPGAGH----TDIISVFEAVGQHARGDISEIQV 182
*************************887....699******************** PP
TIGR00110 166 eeiersacPtagsCsGlftansmacltealGlslPgsstllatsaekkelakksg 220
++ie++a P++gsC+G++tan+ma++ ealG+slPgss+ a+ a+k++ ++g
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3725 183 KQIEEVAIPGPGSCGGMYTANTMASAIEALGMSLPGSSSQDAIGADKASDSFRAG 237
******************************************************* PP
TIGR00110 221 krivelvkknikPrdiltkeafenaitldlalGGstntvLhllaiakeagvklsl 275
++++el+k ++kPrdi+t++afenai +++al Gstn+vLhlla+a+ ++v+l+l
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3725 238 QQVMELLKLDLKPRDIMTRKAFENAIRVVIALAGSTNAVLHLLAMANAVDVELTL 292
******************************************************* PP
TIGR00110 276 ddfdrlsrkvPllaklkPsgkkviedlhraGGvsavlkeldkegllhkdaltvtG 330
ddf +l + P++a+l+Psgk+++ +l + GG++ ++k + +g+lh d+ltvtG
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3725 293 DDFVELGKVSPVVADLRPSGKYMMSELVAIGGIQPLMKRMLDAGMLHGDVLTVTG 347
******************************************************* PP
TIGR00110 331 ktlaetlekvkvlrvdqdvirsldnpvkkegglavLkGnlaeeGavvkiagveed 385
+tlae+l++v+ +++qdvir+ d+p+kk+++l +L+Gnl++ Gav+ki+g+e
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3725 348 QTLAENLASVPDYPAGQDVIRPFDQPIKKDSHLVILRGNLSPTGAVAKITGKEG- 401
******************************************************. PP
TIGR00110 386 ilkfeGpakvfeseeealeailggkvkeGdvvviryeGPkGgPGmremLaPtsal 440
l+feG+a+v++ ee al++il+g+v+ G+v+viryeGPkGgPGmremL Ptsa+
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3725 402 -LRFEGTARVYHGEEGALAGILNGEVQPGEVIVIRYEGPKGGPGMREMLSPTSAV 455
.****************************************************** PP
TIGR00110 441 vglGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaialvedGDkikiDienr 495
+g GLgk+vaLitDGrfsGg++G+++Gh++Pea egG+ialve+GD+i+iD+e r
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3725 456 MGKGLGKEVALITDGRFSGGSHGFVVGHITPEAFEGGPIALVENGDRIIIDAETR 510
******************************************************* PP
TIGR00110 496 kldlevseeelaerrakakkkearevkgaLakyaklvssadkGavld 542
+ ++vs++ laer+ +++++e ++++g+Lakyak vssa++Gav+d
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3725 511 LITVDVSDAVLAERKSRWVRPESKYKRGVLAKYAKTVSSASEGAVTD 557
*********************************************98 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (543 nodes)
Target sequences: 1 (560 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: 0.03u 0.00s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 10.66
//
[ok]
This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 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, or see changes to Amino acid biosynthesis since the publication.
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