Align aconitate hydratase (EC 4.2.1.3) (characterized)
to candidate BWI76_RS11940 BWI76_RS11940 aconitate hydratase 1
Query= BRENDA::P25516
(891 letters)
>FitnessBrowser__Koxy:BWI76_RS11940
Length = 890
Score = 1611 bits (4171), Expect = 0.0
Identities = 796/890 (89%), Positives = 835/890 (93%)
Query: 1 MSSTLREASKDTLQAKDKTYHYYSLPLAAKSLGDITRLPKSLKVLLENLLRWQDGNSVTE 60
MSSTLR ASKDTLQ KDKT+HYYSLPLAAK LGD++RLPKSLKVLLENLLRWQDG+SVT
Sbjct: 1 MSSTLRAASKDTLQVKDKTWHYYSLPLAAKQLGDLSRLPKSLKVLLENLLRWQDGDSVTA 60
Query: 61 EDIHALAGWLKNAHADREIAYRPARVLMQDFTGVPAVVDLAAMREAVKRLGGDTAKVNPL 120
EDIHALAGWLK+AHADREIAYRPARVLMQDFTGVPAVVDLAAMREAVKRLGGDTAKVNPL
Sbjct: 61 EDIHALAGWLKHAHADREIAYRPARVLMQDFTGVPAVVDLAAMREAVKRLGGDTAKVNPL 120
Query: 121 SPVDLVIDHSVTVDRFGDDEAFEENVRLEMERNHERYVFLKWGKQAFSRFSVVPPGTGIC 180
SPVDLVIDHSVTVDRFGDD+AFEENVRLEMERNHERYVFL+WG+QAFSRFSVVPPGTGIC
Sbjct: 121 SPVDLVIDHSVTVDRFGDDDAFEENVRLEMERNHERYVFLRWGQQAFSRFSVVPPGTGIC 180
Query: 181 HQVNLEYLGKAVWSELQDGEWIAYPDTLVGTDSHTTMINGLGVLGWGVGGIEAEAAMLGQ 240
HQVNLEYLG+AVWSE Q+GEW+A+PDTLVGTDSHTTMINGLGVLGWGVGGIEAEAAMLGQ
Sbjct: 181 HQVNLEYLGRAVWSEQQNGEWVAFPDTLVGTDSHTTMINGLGVLGWGVGGIEAEAAMLGQ 240
Query: 241 PVSMLIPDVVGFKLTGKLREGITATDLVLTVTQMLRKHGVVGKFVEFYGDGLDSLPLADR 300
PVSMLIPDVVGFKL+GKLREGITATDLVLTVTQMLRKHGVVGKFVEFYGDGLDSLPLADR
Sbjct: 241 PVSMLIPDVVGFKLSGKLREGITATDLVLTVTQMLRKHGVVGKFVEFYGDGLDSLPLADR 300
Query: 301 ATIANMSPEYGATCGFFPIDAVTLDYMRLSGRSEDQVELVEKYAKAQGMWRNPGDEPIFT 360
ATIANMSPEYGATCGFFPIDAVTLDYMRL+GRSE+QV LVE YAKAQGMWR PGDEP+FT
Sbjct: 301 ATIANMSPEYGATCGFFPIDAVTLDYMRLTGRSEEQVALVEAYAKAQGMWRQPGDEPVFT 360
Query: 361 STLELDMNDVEASLAGPKRPQDRVALPDVPKAFAASNELEVNATHKDRQPVDYVMNGHQY 420
STL LDM VEASLAGPKRPQDRVAL DVP+AFAAS+ELEVN KD++P+DY +NG QY
Sbjct: 361 STLALDMGTVEASLAGPKRPQDRVALGDVPQAFAASSELEVNHAQKDKRPIDYTLNGQQY 420
Query: 421 QLPDGAVVIAAITSCTNTSNPSVLMAAGLLAKKAVTLGLKRQPWVKASLAPGSKVVSDYL 480
LPDGAVVIAAITSCTNTSNPSVLMAAGLLAKKAV GLK QPWVKASLAPGSKVVSDYL
Sbjct: 421 SLPDGAVVIAAITSCTNTSNPSVLMAAGLLAKKAVERGLKPQPWVKASLAPGSKVVSDYL 480
Query: 481 AKAKLTPYLDELGFNLVGYGCTTCIGNSGPLPDPIETAIKKSDLTVGAVLSGNRNFEGRI 540
A AKLTP+LDELGFNLVGYGCTTCIGNSGPLPDPIE AIK+ DLTVGAVLSGNRNFEGRI
Sbjct: 481 AHAKLTPWLDELGFNLVGYGCTTCIGNSGPLPDPIERAIKQGDLTVGAVLSGNRNFEGRI 540
Query: 541 HPLVKTNWLASPPLVVAYALAGNMNINLASEPIGHDRKGDPVYLKDIWPSAQEIARAVEQ 600
HPLVKTNWLASPPLVVAYALAGNMN++L EP+G + G PVYLKDIWPS E+A+AVEQ
Sbjct: 541 HPLVKTNWLASPPLVVAYALAGNMNLDLTREPLGTGKDGQPVYLKDIWPSGIEVAQAVEQ 600
Query: 601 VSTEMFRKEYAEVFEGTAEWKGINVTRSDTYGWQEDSTYIRLSPFFDEMQATPAPVEDIH 660
VSTEMFRKEYAEVFEGTAEWK I V RSDTY WQ DSTYIRLSPFFDEM P PVEDIH
Sbjct: 601 VSTEMFRKEYAEVFEGTAEWKAIKVDRSDTYDWQNDSTYIRLSPFFDEMGVEPKPVEDIH 660
Query: 661 GARILAMLGDSVTTDHISPAGSIKPDSPAGRYLQGRGVERKDFNSYGSRRGNHEVMMRGT 720
GARILAMLGDSVTTDHISPAGSIK DSPAGRYLQ GVER DFNSYGSRRGNHEVMMRGT
Sbjct: 661 GARILAMLGDSVTTDHISPAGSIKADSPAGRYLQNHGVERIDFNSYGSRRGNHEVMMRGT 720
Query: 721 FANIRIRNEMVPGVEGGMTRHLPDSDVVSIYDAAMRYKQEQTPLAVIAGKEYGSGSSRDW 780
FANIRIRNEMVPGVEGGMTRHLPD+ ++IYDAAM YK+E TPLAVIAGKEYGSGSSRDW
Sbjct: 721 FANIRIRNEMVPGVEGGMTRHLPDTQPIAIYDAAMLYKEEGTPLAVIAGKEYGSGSSRDW 780
Query: 781 AAKGPRLLGIRVVIAESFERIHRSNLIGMGILPLEFPQGVTRKTLGLTGEEKIDIGDLQN 840
AAKGPRLLG+RVVIAESFERIHRSNLIGMGILPLEFPQG+TRKTLGL GEE+IDI +LQ
Sbjct: 781 AAKGPRLLGVRVVIAESFERIHRSNLIGMGILPLEFPQGMTRKTLGLNGEERIDISNLQA 840
Query: 841 LQPGATVPVTLTRADGSQEVVPCRCRIDTATELTYYQNDGILHYVIRNML 890
LQPG TVPVTLTRADG QEV+ CRCRIDTATELTYYQNDGILHYVIRNML
Sbjct: 841 LQPGMTVPVTLTRADGRQEVIDCRCRIDTATELTYYQNDGILHYVIRNML 890
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: 2481
Number of extensions: 100
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: 891
Length of database: 890
Length adjustment: 43
Effective length of query: 848
Effective length of database: 847
Effective search space: 718256
Effective search space used: 718256
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 BWI76_RS11940 BWI76_RS11940 (aconitate hydratase 1)
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.2074320.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 1523.2 0.0 0 1523.0 0.0 1.0 1 lcl|FitnessBrowser__Koxy:BWI76_RS11940 BWI76_RS11940 aconitate hydratas
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Koxy:BWI76_RS11940 BWI76_RS11940 aconitate hydratase 1
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1523.0 0.0 0 0 1 876 [] 18 890 .] 18 890 .] 0.99
Alignments for each domain:
== domain 1 score: 1523.0 bits; conditional E-value: 0
TIGR01341 1 kkvyyyslkaleeslekisklpkslrillesvlrnldgskikeedveallkwkkeelkdeeiafkparvvl 71
k+ +yysl+ ++++l+++s+lpksl++lle++lr++dg +++ ed++al+ w k++++d+eia++parv++
lcl|FitnessBrowser__Koxy:BWI76_RS11940 18 KTWHYYSLPLAAKQLGDLSRLPKSLKVLLENLLRWQDGDSVTAEDIHALAGWLKHAHADREIAYRPARVLM 88
578******************************************************************** PP
TIGR01341 72 qdftGvpavvdlaalreavknlgkdpekinplvpvdlvidhsvqvdkageeealeanvelefernkerykf 142
qdftGvpavvdlaa+reavk+lg+d++k+npl+pvdlvidhsv+vd++g+++a+e+nv+le+ern+ery f
lcl|FitnessBrowser__Koxy:BWI76_RS11940 89 QDFTGVPAVVDLAAMREAVKRLGGDTAKVNPLSPVDLVIDHSVTVDRFGDDDAFEENVRLEMERNHERYVF 159
*********************************************************************** PP
TIGR01341 143 lkwakkafknlkvvppgtGivhqvnleylakvvfeaekdgellaypdslvGtdshttminGlGvlGwGvGG 213
l+w+++af++++vvppgtGi+hqvnleyl+++v++++++ge++a+pd+lvGtdshttminGlGvlGwGvGG
lcl|FitnessBrowser__Koxy:BWI76_RS11940 160 LRWGQQAFSRFSVVPPGTGICHQVNLEYLGRAVWSEQQNGEWVAFPDTLVGTDSHTTMINGLGVLGWGVGG 230
*********************************************************************** PP
TIGR01341 214 ieaeaallGqpvslsvpeviGvkltGklreGvtatdlvltvtellrkkgvvgkfveffGeglkelsladra 284
ieaeaa+lGqpvs+ +p+v+G+kl GklreG+tatdlvltvt++lrk+gvvgkfvef+G+gl++l+ladra
lcl|FitnessBrowser__Koxy:BWI76_RS11940 231 IEAEAAMLGQPVSMLIPDVVGFKLSGKLREGITATDLVLTVTQMLRKHGVVGKFVEFYGDGLDSLPLADRA 301
*********************************************************************** PP
TIGR01341 285 tianmapeyGataaffpiddvtlqylrltgrdedkvelvekylkaqelfvddseepkytdvveldlsdvea 355
tianm+peyGat++ffpid+vtl+y+rltgr+e++v lve+y+kaq+++++ ++ep++t+++ ld+ +vea
lcl|FitnessBrowser__Koxy:BWI76_RS11940 302 TIANMSPEYGATCGFFPIDAVTLDYMRLTGRSEEQVALVEAYAKAQGMWRQPGDEPVFTSTLALDMGTVEA 372
*********************************************************************** PP
TIGR01341 356 svaGpkrpqdrvalkevkaafkss..lesnagekglalrkeakekklegkeaelkdgavviaaitsctnts 424
s+aGpkrpqdrval +v++af++s le+n ++k+ k++ +++l+g++++l dgavviaaitsctnts
lcl|FitnessBrowser__Koxy:BWI76_RS11940 373 SLAGPKRPQDRVALGDVPQAFAASseLEVNHAQKD----KRPIDYTLNGQQYSLPDGAVVIAAITSCTNTS 439
*********************98845777777777....******************************** PP
TIGR01341 425 npsvllgagllakkavelGlkvkpyvktslapGskvvtdylaesgllpyleelGfnlvGyGcttciGnsGp 495
npsvl++agllakkave Glk +p+vk+slapGskvv+dyla+++l+p+l+elGfnlvGyGcttciGnsGp
lcl|FitnessBrowser__Koxy:BWI76_RS11940 440 NPSVLMAAGLLAKKAVERGLKPQPWVKASLAPGSKVVSDYLAHAKLTPWLDELGFNLVGYGCTTCIGNSGP 510
*********************************************************************** PP
TIGR01341 496 leeeveeaikendlevsavlsGnrnfegrihplvkanylaspplvvayalaGtvdidlekepigtdkdGkk 566
l++ +e aik++dl+v avlsGnrnfegrihplvk+n+laspplvvayalaG++++dl++ep+gt+kdG++
lcl|FitnessBrowser__Koxy:BWI76_RS11940 511 LPDPIERAIKQGDLTVGAVLSGNRNFEGRIHPLVKTNWLASPPLVVAYALAGNMNLDLTREPLGTGKDGQP 581
*********************************************************************** PP
TIGR01341 567 vylkdiwpsakeiaelvkkavkkelfkkeyeevtegnerwnelevtssdlyewdekstyireppffeelkl 637
vylkdiwps e+a++ ++v++e+f+key+ev+eg+++w+ ++v +sd+y+w+++styir++pff+e+ +
lcl|FitnessBrowser__Koxy:BWI76_RS11940 582 VYLKDIWPSGIEVAQA-VEQVSTEMFRKEYAEVFEGTAEWKAIKVDRSDTYDWQNDSTYIRLSPFFDEMGV 651
**************95.578*************************************************** PP
TIGR01341 638 epeevedikgarillllGdsittdhispaGsikkdspaakylkekGverrdfnsyGsrrGnhevmlrGtfa 708
ep+ vedi+garil++lGds+ttdhispaGsik dspa++yl+++Gver dfnsyGsrrGnhevm+rGtfa
lcl|FitnessBrowser__Koxy:BWI76_RS11940 652 EPKPVEDIHGARILAMLGDSVTTDHISPAGSIKADSPAGRYLQNHGVERIDFNSYGSRRGNHEVMMRGTFA 722
*********************************************************************** PP
TIGR01341 709 niriknklvkgkeGgltvylpdsevvsvydaamkykkegvplvvlaGkeyGsGssrdwaakgtkllGvkav 779
niri+n++v+g eGg+t++lpd++ +++ydaam yk+eg+pl+v+aGkeyGsGssrdwaakg++llGv++v
lcl|FitnessBrowser__Koxy:BWI76_RS11940 723 NIRIRNEMVPGVEGGMTRHLPDTQPIAIYDAAMLYKEEGTPLAVIAGKEYGSGSSRDWAAKGPRLLGVRVV 793
*********************************************************************** PP
TIGR01341 780 iaesferihrsnlvgmGvlplefkqgedaetlgltgeetidvddieelkpkkevtvelvkedgeketveav 850
iaesferihrsnl+gmG+lplef+qg +++tlgl+gee+id+++++ l+p+ +v+v+l+++dg +e+++++
lcl|FitnessBrowser__Koxy:BWI76_RS11940 794 IAESFERIHRSNLIGMGILPLEFPQGMTRKTLGLNGEERIDISNLQALQPGMTVPVTLTRADGRQEVIDCR 864
*********************************************************************** PP
TIGR01341 851 lridtevelayvkkgGilqyvlrkll 876
+ridt++el+y++++Gil+yv+r++l
lcl|FitnessBrowser__Koxy:BWI76_RS11940 865 CRIDTATELTYYQNDGILHYVIRNML 890
************************97 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (876 nodes)
Target sequences: 1 (890 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 0.02s 00:00:00.05 Elapsed: 00:00:00.04
# Mc/sec: 16.97
//
[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