Align aconitate hydratase (EC 4.2.1.3) (characterized)
to candidate H281DRAFT_06210 H281DRAFT_06210 aconitate hydratase
Query= BRENDA::P25516
(891 letters)
>FitnessBrowser__Burk376:H281DRAFT_06210
Length = 898
Score = 878 bits (2268), Expect = 0.0
Identities = 456/887 (51%), Positives = 597/887 (67%), Gaps = 29/887 (3%)
Query: 12 TLQAKDKTYHYYSLPLA-AKSLGDITRLPKSLKVLLENLLRWQDGNSVTEEDIHALAGWL 70
TL+ Y L A A+ ++ LP SL++LLEN +R + G +D+ A+ WL
Sbjct: 13 TLETASGPLRYADLKRAEAQGFAPLSELPVSLRILLENAMR-RGG----VDDVAAIRDWL 67
Query: 71 KNAHADREIAYRPARVLMQDFTGVPAVVDLAAMREAVKRLGGDTAKVNPLSPVDLVIDHS 130
+DREI++ P RVLM D + VP V DLAAMR+AV++ GGD+ +VNPL PVD+V+DHS
Sbjct: 68 TRRESDREISFFPVRVLMPDSSAVPLVADLAAMRDAVRKKGGDSWRVNPLIPVDIVVDHS 127
Query: 131 VTVDRFGDDEAFEENVRLEMERNHERYVFLKWGKQAFSRFSVVPPGTGICHQVNLEYLGK 190
D G +AF+ N+ LE +RNHERY FLKW + AF VVPP TGI HQVNLE+L
Sbjct: 128 AITDHAGRSDAFDLNLALEYQRNHERYAFLKWAQNAFDNVRVVPPATGIVHQVNLEFLAA 187
Query: 191 AVWSELQDGEWIAYPDTLVGTDSHTTMINGLGVLGWGVGGIEAEAAMLGQPVSMLIPDVV 250
V + + D PDTLVG DSHTTM+N +GVLGWGVGGIEA AA+LGQP+SML+P V+
Sbjct: 188 GVQTVVIDDVTFVVPDTLVGMDSHTTMVNSIGVLGWGVGGIEAAAAILGQPISMLLPRVI 247
Query: 251 GFKLTGKLREGITATDLVLTVTQMLRKHGVVGKFVEFYGDGLDSLPLADRATIANMSPEY 310
G +++G+ R G+T TD+VL++T+ LR VVG FVEF+G+GLD+LP++DRATIANM+PE
Sbjct: 248 GCRISGRPRSGVTCTDIVLSLTEFLRGKKVVGCFVEFFGEGLDNLPVSDRATIANMAPEA 307
Query: 311 GATCGFFPIDAVTLDYMRLSGRSEDQVELVEKYAKAQGMWR---NPGDEPI-FTSTLELD 366
GAT FFP DA T++Y+ +GRS +QV + E KAQG+WR +E I ++ LE D
Sbjct: 308 GATMCFFPPDAATIEYLHATGRSREQVAVAEAVLKAQGIWRPEAGADEERIAYSDRLEFD 367
Query: 367 MNDVEASLAGPKRPQDRVALPDVPKAFAASNELEVNATHKDRQPVDYVMNGHQYQLPDGA 426
++ V S+AGPKRPQDRV L DV F H+ ++ + L +G+
Sbjct: 368 LSAVTPSMAGPKRPQDRVDLKDVSARF-----------HR-----EFGLTAEGRGLTNGS 411
Query: 427 VVIAAITSCTNTSNPSVLMAAGLLAKKAVTLGLKRQPWVKASLAPGSKVVSDYLAKAKLT 486
VVIAAITSCTNTSN ++ AGL+A+ G+K + WVK SL+PGS+VV+DYL ++ L
Sbjct: 412 VVIAAITSCTNTSNARAMIGAGLIARNLRARGVKPKAWVKTSLSPGSRVVTDYLRESGLQ 471
Query: 487 PYLDELGFNLVGYGCTTCIGNSGPLPDPIETAIKKSDLTVGAVLSGNRNFEGRIHPLVKT 546
LD LGFNL GYGC TC G+SG L + I L V VLSGNRNFEGR HPL +
Sbjct: 472 DDLDSLGFNLTGYGCMTCAGSSGQLDAEVARRILSEGLVVATVLSGNRNFEGRTHPLARA 531
Query: 547 NWLASPPLVVAYALAGNMNINLASEPIGHDRKGDPVYLKDIWPSAQEIARAVEQVST-EM 605
N+L SP LVVAYA AG + +L +EPI + G PV L D+WP +I ++ T M
Sbjct: 532 NFLGSPALVVAYACAGTILRDLTTEPIADEADGQPVMLADVWPDDADIDAIFRRIVTLTM 591
Query: 606 FRKEYAEVFEGTAEWKGINVTRSDTYGWQEDSTYIRLSPFFDEMQATPA-PVEDIHGARI 664
F++ YA F+G A W+ I D + W + STYIR P+FD A + +I GAR
Sbjct: 592 FKRVYATAFQGEARWQRIAAASGDHFDWDQASTYIRRPPYFDAGFADDGFGMANIVGARA 651
Query: 665 LAMLGDSVTTDHISPAGSIKPDSPAGRYLQGRGVERKDFNSYGSRRGNHEVMMRGTFANI 724
L MLGDS+TTDHISP G I+ ++ AGR+L G GV DFN+ SRR NH+VMMRGTFAN+
Sbjct: 652 LLMLGDSITTDHISPVGVIRSETEAGRFLHGAGVAPSDFNTLLSRRANHDVMMRGTFANV 711
Query: 725 RIRNEMVPGVEGGMTRHLPDSDVVSIYDAAMRYKQEQTPLAVIAGKEYGSGSSRDWAAKG 784
R+RNEM P EG +RH+P DV+ ++ AA RY+ E+ PL VIAG +YG+GSSRDWAAKG
Sbjct: 712 RLRNEMTPDREGPWSRHVPSGDVMRVFQAASRYRDERVPLIVIAGADYGAGSSRDWAAKG 771
Query: 785 PRLLGIRVVIAESFERIHRSNLIGMGILPLEFPQGVTRKTLGLTGEEKIDIGDLQN-LQP 843
PRLLG+R VIAESFERIHRSNL+GMGILPL+FP G TRKTLGLTGEE I ++ LQP
Sbjct: 772 PRLLGVRAVIAESFERIHRSNLVGMGILPLQFPPGTTRKTLGLTGEESFTIFGIEGALQP 831
Query: 844 GATVPVTLTRADGSQEVVPCRCRIDTATELTYYQNDGILHYVIRNML 890
+ ++RA+G+++ + CR+D E+ +Y++ G+L Y+ +L
Sbjct: 832 HQRIECEVSRANGARDSITLICRLDIPREIAWYRHGGVLQYIAAQLL 878
Lambda K H
0.317 0.135 0.401
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: 1946
Number of extensions: 90
Number of successful extensions: 8
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: 891
Length of database: 898
Length adjustment: 43
Effective length of query: 848
Effective length of database: 855
Effective search space: 725040
Effective search space used: 725040
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: 56 (26.2 bits)
Align candidate H281DRAFT_06210 H281DRAFT_06210 (aconitate hydratase)
to HMM TIGR01341 (acnA: aconitate hydratase 1 (EC 4.2.1.3))
# 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/TIGR01341.hmm
# target sequence database: /tmp/gapView.24499.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: TIGR01341 [M=876]
Accession: TIGR01341
Description: aconitase_1: aconitate hydratase 1
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 1096.5 0.0 0 1094.4 0.0 1.7 1 lcl|FitnessBrowser__Burk376:H281DRAFT_06210 H281DRAFT_06210 aconitate hydrat
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Burk376:H281DRAFT_06210 H281DRAFT_06210 aconitate hydratase
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1094.4 0.0 0 0 5 875 .. 23 877 .. 20 878 .. 0.96
Alignments for each domain:
== domain 1 score: 1094.4 bits; conditional E-value: 0
TIGR01341 5 yyslkalees.lekisklpkslrillesvlrnldgskikeedveallkwkkeelkdeeiafkparv 69
y lk++e + +s+lp slrille+++r+ +dv a+ +w + +d+ei+f p rv
lcl|FitnessBrowser__Burk376:H281DRAFT_06210 23 YADLKRAEAQgFAPLSELPVSLRILLENAMRRGG-----VDDVAAIRDWLTRRESDREISFFPVRV 83
677887776646789****************864.....4799*********************** PP
TIGR01341 70 vlqdftGvpavvdlaalreavknlgkdpekinplvpvdlvidhsvqvdkageeealeanvelefer 135
++ d + vp+v dlaa+r+av++ g+d+ ++npl+pvd+v+dhs d+ag ++a++ n+ le++r
lcl|FitnessBrowser__Burk376:H281DRAFT_06210 84 LMPDSSAVPLVADLAAMRDAVRKKGGDSWRVNPLIPVDIVVDHSAITDHAGRSDAFDLNLALEYQR 149
****************************************************************** PP
TIGR01341 136 nkerykflkwakkafknlkvvppgtGivhqvnleylakvvfeaekdgellaypdslvGtdshttmi 201
n+ery+flkwa++af n++vvpp+tGivhqvnle+la v + d +++ pd+lvG dshttm+
lcl|FitnessBrowser__Burk376:H281DRAFT_06210 150 NHERYAFLKWAQNAFDNVRVVPPATGIVHQVNLEFLAAGVQTVVIDDVTFVVPDTLVGMDSHTTMV 215
****************************************************************** PP
TIGR01341 202 nGlGvlGwGvGGieaeaallGqpvslsvpeviGvkltGklreGvtatdlvltvtellrkkgvvgkf 267
n +GvlGwGvGGiea aa+lGqp+s+ +p viG ++ G+ r Gvt td+vl +te+lr k vvg f
lcl|FitnessBrowser__Burk376:H281DRAFT_06210 216 NSIGVLGWGVGGIEAAAAILGQPISMLLPRVIGCRISGRPRSGVTCTDIVLSLTEFLRGKKVVGCF 281
****************************************************************** PP
TIGR01341 268 veffGeglkelsladratianmapeyGataaffpiddvtlqylrltgrdedkvelvekylkaqelf 333
veffGegl++l+++dratianmape Gat++ffp d+ t++yl+ tgr+ ++v + e+ lkaq+++
lcl|FitnessBrowser__Burk376:H281DRAFT_06210 282 VEFFGEGLDNLPVSDRATIANMAPEAGATMCFFPPDAATIEYLHATGRSREQVAVAEAVLKAQGIW 347
****************************************************************** PP
TIGR01341 334 vd..dsee..pkytdvveldlsdveasvaGpkrpqdrvalkevkaafksslesnagekglalrkea 395
+ ++e + y+d +e dls v +s+aGpkrpqdrv+lk+v a f++ +++l+
lcl|FitnessBrowser__Burk376:H281DRAFT_06210 348 RPeaGADEerIAYSDRLEFDLSAVTPSMAGPKRPQDRVDLKDVSARFHR---------EFGLT--- 401
973322224599*********************************8865.........44443... PP
TIGR01341 396 kekklegkeaelkdgavviaaitsctntsnpsvllgagllakkavelGlkvkpyvktslapGskvv 461
+ l++g+vviaaitsctntsn ++gagl+a+ G+k k +vktsl+pGs+vv
lcl|FitnessBrowser__Burk376:H281DRAFT_06210 402 ------AEGRGLTNGSVVIAAITSCTNTSNARAMIGAGLIARNLRARGVKPKAWVKTSLSPGSRVV 461
......34556899**************************************************** PP
TIGR01341 462 tdylaesgllpyleelGfnlvGyGcttciGnsGpleeeveeaikendlevsavlsGnrnfegrihp 527
tdyl esgl++ l+ lGfnl GyGc tc G sG+l+ ev+ i ++l+v++vlsGnrnfegr hp
lcl|FitnessBrowser__Burk376:H281DRAFT_06210 462 TDYLRESGLQDDLDSLGFNLTGYGCMTCAGSSGQLDAEVARRILSEGLVVATVLSGNRNFEGRTHP 527
****************************************************************** PP
TIGR01341 528 lvkanylaspplvvayalaGtvdidlekepigtdkdGkkvylkdiwpsakeiaelvkkavkkelfk 593
l +an+l sp lvvaya aGt+ dl++epi+ + dG++v l d+wp +i+++ ++ v+ +fk
lcl|FitnessBrowser__Burk376:H281DRAFT_06210 528 LARANFLGSPALVVAYACAGTILRDLTTEPIADEADGQPVMLADVWPDDADIDAIFRRIVTLTMFK 593
****************************************************************** PP
TIGR01341 594 keyeevtegnerwnelevtssdlyewdekstyireppffee.lklepeevedikgarillllGdsi 658
+ y++ ++g++rw+++ ++s+d ++wd+ styir+pp+f+ + + + +i gar ll+lGdsi
lcl|FitnessBrowser__Burk376:H281DRAFT_06210 594 RVYATAFQGEARWQRIAAASGDHFDWDQASTYIRRPPYFDAgFADDGFGMANIVGARALLMLGDSI 659
***************************************962566677999*************** PP
TIGR01341 659 ttdhispaGsikkdspaakylkekGverrdfnsyGsrrGnhevmlrGtfaniriknklvkgkeGgl 724
ttdhisp G i+ ++ a+++l+ Gv + dfn+ srr nh+vm+rGtfan+r++n++ + +eG+
lcl|FitnessBrowser__Burk376:H281DRAFT_06210 660 TTDHISPVGVIRSETEAGRFLHGAGVAPSDFNTLLSRRANHDVMMRGTFANVRLRNEMTPDREGPW 725
****************************************************************** PP
TIGR01341 725 tvylpdsevvsvydaamkykkegvplvvlaGkeyGsGssrdwaakgtkllGvkaviaesferihrs 790
++++p ++v+ v++aa +y++e+vpl+v+aG++yG+Gssrdwaakg++llGv+aviaesferihrs
lcl|FitnessBrowser__Burk376:H281DRAFT_06210 726 SRHVPSGDVMRVFQAASRYRDERVPLIVIAGADYGAGSSRDWAAKGPRLLGVRAVIAESFERIHRS 791
****************************************************************** PP
TIGR01341 791 nlvgmGvlplefkqgedaetlgltgeetidvddie.elkpkkevtvelvkedgeketveavlridt 855
nlvgmG+lpl+f+ g++++tlgltgee + +ie l+p+++++ e+ +++g + +++ +r+d
lcl|FitnessBrowser__Burk376:H281DRAFT_06210 792 NLVGMGILPLQFPPGTTRKTLGLTGEESFTIFGIEgALQPHQRIECEVSRANGARDSITLICRLDI 857
*****************************999986479**************************** PP
TIGR01341 856 evelayvkkgGilqyvlrkl 875
+ e+a++++gG+lqy+ +l
lcl|FitnessBrowser__Burk376:H281DRAFT_06210 858 PREIAWYRHGGVLQYIAAQL 877
***************97665 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (876 nodes)
Target sequences: 1 (898 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: 0.14u 0.03s 00:00:00.17 Elapsed: 00:00:00.16
# Mc/sec: 4.65
//
[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