Align Aconitate hydratase (EC 4.2.1.3) (characterized)
to candidate AO353_00565 AO353_00565 aconitate hydratase
Query= reanno::Marino:GFF3491
(919 letters)
>FitnessBrowser__pseudo3_N2E3:AO353_00565
Length = 916
Score = 1300 bits (3364), Expect = 0.0
Identities = 648/915 (70%), Positives = 748/915 (81%), Gaps = 8/915 (0%)
Query: 7 SKDSLNTLSSLDAGGKTFHYYSLPKAADTLGDLNRLPFSLKVLMENLLRNEDGTTVDRSH 66
S DSL TL +L KT+HY+SLP+AA +LGDL++LP SLKVL+ENLLR ED TV +
Sbjct: 3 SLDSLKTLKTLKIDDKTYHYFSLPEAAKSLGDLDKLPMSLKVLLENLLRWEDEKTVTGAD 62
Query: 67 IDAMVQWMKDRHSDTEIQFRPARVLMQDFTGVPGVVDLAAMREAVQAAGKDPAMINPLSP 126
+ A+ W+K+R SD EIQ+RPARVLMQDFTGVP VVDLAAMR A+ AG DP INPLSP
Sbjct: 63 LKALAAWLKERRSDREIQYRPARVLMQDFTGVPAVVDLAAMRAAMAKAGGDPQRINPLSP 122
Query: 127 VDLVIDHSVMVDKFGDASSFKDNVAIEMERNQERYEFLRWGQQAFDNFRVVPPGTGICHQ 186
VDLVIDHSVMVDKF +++F NV IEM+RN ERY FLRWGQ AFDNF VVPPGTGICHQ
Sbjct: 123 VDLVIDHSVMVDKFASSTAFTQNVDIEMQRNGERYAFLRWGQSAFDNFSVVPPGTGICHQ 182
Query: 187 VNLEYLGKTVWQKDQDGKTIAYPDTLVGTDSHTTMINGLGILGWGVGGIEAEAAMLGQPV 246
VNLEYLG+TVW KD+D +T A+PDTLVGTDSHTTMINGLG+LGWGVGGIEAEAAMLGQPV
Sbjct: 183 VNLEYLGRTVWTKDEDDRTYAFPDTLVGTDSHTTMINGLGVLGWGVGGIEAEAAMLGQPV 242
Query: 247 SMLIPEVVGFKITGKLREGITATDLVLTVTEMLRKKGVVGKFVEFYGDGLKDMPVADRAT 306
SMLIPEV+GFK+TGKL+EGITATDLVLTVT+MLRKKGVVGKFVEFYGDGL ++P+ADRAT
Sbjct: 243 SMLIPEVIGFKLTGKLKEGITATDLVLTVTQMLRKKGVVGKFVEFYGDGLAELPLADRAT 302
Query: 307 IANMAPEYGATCGFFPVDEQTIKYMRLTGREEEQLELVEAYAKAQGLWREPGHEPVYTDN 366
IANMAPEYGATCGFFPVDE T++Y+RL+GR ++LVEAY K QGLWR PG EPV+TD+
Sbjct: 303 IANMAPEYGATCGFFPVDEVTLEYLRLSGRPSAVVKLVEAYCKTQGLWRLPGQEPVFTDS 362
Query: 367 LELDMGEVEASLAGPKRPQDRVALKNMKSSFELLMETAEGPAE---NREANLESEGGQ-T 422
L LDM VEASLAGPKRPQDRV+L N+ +F + PA E LESEGG
Sbjct: 363 LALDMSSVEASLAGPKRPQDRVSLPNVAQAFTDFLGLQVKPARPTSKEEGRLESEGGGGV 422
Query: 423 AVGVDDSYKHHASQPLEMNGEKSRLDPGAVVIAAITSCTNTSNPSVMMAAGLIAQKAVQK 482
AVG D + E G+ RL GAVVIAAITSCTNTSNPSVMMAAGL+A+KAV+K
Sbjct: 423 AVGNADLV---SEADYEYEGQTYRLKNGAVVIAAITSCTNTSNPSVMMAAGLVAKKAVEK 479
Query: 483 GLSTKPWVKTSLAPGSKVVTDYLKVGGFQDDLDKLGFNLVGYGCTTCIGNSGPLPDAVEK 542
GL KPWVK+SLAPGSKVVTDY K G LD+LGF+LVGYGCTTCIGNSGPL + +EK
Sbjct: 480 GLKRKPWVKSSLAPGSKVVTDYYKAAGLTQYLDELGFSLVGYGCTTCIGNSGPLLEPIEK 539
Query: 543 AISDGDLTVASVLSGNRNFEGRVHPLVKTNWLASPPLVVAYALAGNVRLDLSQDPLGNDK 602
AI DL VASVLSGNRNFEGRVHPLVKTNWLASPPLVVAYALAG+VR+D+S +PLG K
Sbjct: 540 AIQSSDLAVASVLSGNRNFEGRVHPLVKTNWLASPPLVVAYALAGSVRMDISSEPLGEGK 599
Query: 603 DGNPVYLKDLWPSQQEIAEAVEKVKTDMFRKEYAEVFDGDATWKSIKVPESKVYEWSDKS 662
DG PVYL+D+WPS +EIA+AV +V T MF KEYAEVF GDA W++I+VP++ Y W S
Sbjct: 600 DGKPVYLRDIWPSSKEIADAVAQVDTAMFHKEYAEVFAGDAQWQAIEVPQAATYVWQKDS 659
Query: 663 TYIQHPPFFEGLKEEPDAIDDIKDANILALLGDSVTTDHISPAGSFKPDTPAGKYLQEHG 722
TYIQHPPFF+ + I DI A ILALLGDSVTTDHISPAG+ K D+PAG+YL+E G
Sbjct: 660 TYIQHPPFFDDISGPLPVIQDISGARILALLGDSVTTDHISPAGNIKADSPAGRYLREQG 719
Query: 723 VEPKDFNSYGSRRGNHEVMMRGTFANVRIRNEMLDGVEGGYTKFVPTGEQMAIYDAAMKY 782
VEP+DFNSYGSRRGNHEVMMRGTFAN+RIRNEML G EGG T ++PTGE++AIYDAAM+Y
Sbjct: 720 VEPRDFNSYGSRRGNHEVMMRGTFANIRIRNEMLGGEEGGNTLYIPTGEKLAIYDAAMRY 779
Query: 783 QEKGTPLVVIAGKEYGTGSSRDWAAKGTRLLGVKAVVAESYERIHRSNLIGMGVMPLQFP 842
Q GTPLVVIAG+EYGTGSSRDWAAKGT LLGVKAV+AES+ERIHRSNL+GMGV+PLQF
Sbjct: 780 QAAGTPLVVIAGQEYGTGSSRDWAAKGTNLLGVKAVIAESFERIHRSNLVGMGVLPLQFK 839
Query: 843 EGTDRKSLKLTGEETISIEGLSG-EIKPGQTLKMTVKYKDGSTETCELKSRIDTANEAVY 901
+RKSL LTG+ET+ I+GL+G E+ P L + + +DGS+E E+ RIDT NE Y
Sbjct: 840 LDQNRKSLNLTGKETLDIQGLTGVELTPRMNLTLVITREDGSSEKVEVLCRIDTLNEVEY 899
Query: 902 FKHGGILHYVVREML 916
FK GGILHYV+R+++
Sbjct: 900 FKAGGILHYVLRQLI 914
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: 2300
Number of extensions: 98
Number of successful extensions: 4
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: 919
Length of database: 916
Length adjustment: 43
Effective length of query: 876
Effective length of database: 873
Effective search space: 764748
Effective search space used: 764748
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: 42 (22.0 bits)
S2: 57 (26.6 bits)
Align candidate AO353_00565 AO353_00565 (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.7777.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 1417.2 0.0 0 1416.9 0.0 1.1 1 lcl|FitnessBrowser__pseudo3_N2E3:AO353_00565 AO353_00565 aconitate hydratase
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo3_N2E3:AO353_00565 AO353_00565 aconitate hydratase
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1416.9 0.0 0 0 1 876 [] 18 914 .. 18 914 .. 0.97
Alignments for each domain:
== domain 1 score: 1416.9 bits; conditional E-value: 0
TIGR01341 1 kkvyyyslkaleeslekisklpkslrillesvlrnldgskikeedveallkwkkeelkdeeiafk 65
k+++y+sl+++++sl++++klp sl++lle++lr+ d+++++ d++al+ w ke +d+ei+++
lcl|FitnessBrowser__pseudo3_N2E3:AO353_00565 18 KTYHYFSLPEAAKSLGDLDKLPMSLKVLLENLLRWEDEKTVTGADLKALAAWLKERRSDREIQYR 82
689************************************************************** PP
TIGR01341 66 parvvlqdftGvpavvdlaalreavknlgkdpekinplvpvdlvidhsvqvdkageeealeanve 130
parv++qdftGvpavvdlaa+r a+++ g+dp++inpl+pvdlvidhsv vdk+ +++a+ +nv+
lcl|FitnessBrowser__pseudo3_N2E3:AO353_00565 83 PARVLMQDFTGVPAVVDLAAMRAAMAKAGGDPQRINPLSPVDLVIDHSVMVDKFASSTAFTQNVD 147
***************************************************************** PP
TIGR01341 131 lefernkerykflkwakkafknlkvvppgtGivhqvnleylakvvfeaekdgellaypdslvGtd 195
+e++rn ery+fl+w++ af n++vvppgtGi+hqvnleyl++ v+++++d +++a+pd+lvGtd
lcl|FitnessBrowser__pseudo3_N2E3:AO353_00565 148 IEMQRNGERYAFLRWGQSAFDNFSVVPPGTGICHQVNLEYLGRTVWTKDEDDRTYAFPDTLVGTD 212
***************************************************************** PP
TIGR01341 196 shttminGlGvlGwGvGGieaeaallGqpvslsvpeviGvkltGklreGvtatdlvltvtellrk 260
shttminGlGvlGwGvGGieaeaa+lGqpvs+ +peviG+kltGkl+eG+tatdlvltvt++lrk
lcl|FitnessBrowser__pseudo3_N2E3:AO353_00565 213 SHTTMINGLGVLGWGVGGIEAEAAMLGQPVSMLIPEVIGFKLTGKLKEGITATDLVLTVTQMLRK 277
***************************************************************** PP
TIGR01341 261 kgvvgkfveffGeglkelsladratianmapeyGataaffpiddvtlqylrltgrdedkvelvek 325
kgvvgkfvef+G+gl+el+ladratianmapeyGat++ffp+d+vtl+ylrl+gr++ v+lve+
lcl|FitnessBrowser__pseudo3_N2E3:AO353_00565 278 KGVVGKFVEFYGDGLAELPLADRATIANMAPEYGATCGFFPVDEVTLEYLRLSGRPSAVVKLVEA 342
***************************************************************** PP
TIGR01341 326 ylkaqelfvddseepkytdvveldlsdveasvaGpkrpqdrvalkevkaafksslesnagekgla 390
y+k+q+l++ ++ep++td + ld+s+veas+aGpkrpqdrv+l +v +af+ l ++ +
lcl|FitnessBrowser__pseudo3_N2E3:AO353_00565 343 YCKTQGLWRLPGQEPVFTDSLALDMSSVEASLAGPKRPQDRVSLPNVAQAFTDFLGLQVKPARPT 407
****************************************************9976554433322 PP
TIGR01341 391 lr....................keakekklegkeaelkdgavviaaitsctntsnpsvllgagll 435
+ ++ eg++++lk+gavviaaitsctntsnpsv+++agl+
lcl|FitnessBrowser__pseudo3_N2E3:AO353_00565 408 SKeegrleseggggvavgnadlVSEADYEYEGQTYRLKNGAVVIAAITSCTNTSNPSVMMAAGLV 472
2224445688888888888766555667778********************************** PP
TIGR01341 436 akkavelGlkvkpyvktslapGskvvtdylaesgllpyleelGfnlvGyGcttciGnsGpleeev 500
akkave Glk+kp+vk+slapGskvvtdy + +gl++yl+elGf+lvGyGcttciGnsGpl e +
lcl|FitnessBrowser__pseudo3_N2E3:AO353_00565 473 AKKAVEKGLKRKPWVKSSLAPGSKVVTDYYKAAGLTQYLDELGFSLVGYGCTTCIGNSGPLLEPI 537
***************************************************************** PP
TIGR01341 501 eeaikendlevsavlsGnrnfegrihplvkanylaspplvvayalaGtvdidlekepigtdkdGk 565
e+ai+ +dl v++vlsGnrnfegr+hplvk+n+laspplvvayalaG+v +d+++ep+g +kdGk
lcl|FitnessBrowser__pseudo3_N2E3:AO353_00565 538 EKAIQSSDLAVASVLSGNRNFEGRVHPLVKTNWLASPPLVVAYALAGSVRMDISSEPLGEGKDGK 602
***************************************************************** PP
TIGR01341 566 kvylkdiwpsakeiaelvkkavkkelfkkeyeevtegnerwnelevtssdlyewdekstyirepp 630
+vyl+diwps keia++v +v + +f+key+ev+ g+++w+ +ev++ ++y w+++styi++pp
lcl|FitnessBrowser__pseudo3_N2E3:AO353_00565 603 PVYLRDIWPSSKEIADAV-AQVDTAMFHKEYAEVFAGDAQWQAIEVPQAATYVWQKDSTYIQHPP 666
****************65.689******************************************* PP
TIGR01341 631 ffeelklepeevedikgarillllGdsittdhispaGsikkdspaakylkekGverrdfnsyGsr 695
ff++++ ++di garil+llGds+ttdhispaG+ik dspa++yl+e+Gve+rdfnsyGsr
lcl|FitnessBrowser__pseudo3_N2E3:AO353_00565 667 FFDDISGPLPVIQDISGARILALLGDSVTTDHISPAGNIKADSPAGRYLREQGVEPRDFNSYGSR 731
*******88999***************************************************** PP
TIGR01341 696 rGnhevmlrGtfaniriknklvkgkeGgltvylpdsevvsvydaamkykkegvplvvlaGkeyGs 760
rGnhevm+rGtfaniri+n+++ g+eGg t+y+p++e++++ydaam+y+ g+plvv+aG+eyG+
lcl|FitnessBrowser__pseudo3_N2E3:AO353_00565 732 RGNHEVMMRGTFANIRIRNEMLGGEEGGNTLYIPTGEKLAIYDAAMRYQAAGTPLVVIAGQEYGT 796
***************************************************************** PP
TIGR01341 761 GssrdwaakgtkllGvkaviaesferihrsnlvgmGvlplefkqgedaetlgltgeetidvddie 825
Gssrdwaakgt+llGvkaviaesferihrsnlvgmGvlpl+fk +++++l+ltg+et+d+++++
lcl|FitnessBrowser__pseudo3_N2E3:AO353_00565 797 GSSRDWAAKGTNLLGVKAVIAESFERIHRSNLVGMGVLPLQFKLDQNRKSLNLTGKETLDIQGLT 861
***************************************************************86 PP
TIGR01341 826 ..elkpkkevtvelvkedgeketveavlridtevelayvkkgGilqyvlrkll 876
el p+ ++t+++++edg+ e ve+ +ridt e++y+k gGil+yvlr+l+
lcl|FitnessBrowser__pseudo3_N2E3:AO353_00565 862 gvELTPRMNLTLVITREDGSSEKVEVLCRIDTLNEVEYFKAGGILHYVLRQLI 914
33678*********************************************975 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (876 nodes)
Target sequences: 1 (916 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: 0.07u 0.03s 00:00:00.10 Elapsed: 00:00:00.09
# Mc/sec: 8.64
//
[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