Align Aconitate hydratase (EC 4.2.1.3) (characterized)
to candidate Pf1N1B4_3888 Aconitate hydratase (EC 4.2.1.3)
Query= reanno::Marino:GFF3491
(919 letters)
>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3888
Length = 913
Score = 1311 bits (3394), Expect = 0.0
Identities = 649/916 (70%), Positives = 755/916 (82%), Gaps = 13/916 (1%)
Query: 7 SKDSLNTLSSLDAGGKTFHYYSLPKAADTLGDLNRLPFSLKVLMENLLRNEDGTTVDRSH 66
S DSL TL +L KT+HY+SLP+AA +LGDL++LP SLKVL+ENLLR ED TV +
Sbjct: 3 SLDSLKTLKTLQVDDKTYHYFSLPEAAKSLGDLDKLPMSLKVLLENLLRWEDEKTVTGAD 62
Query: 67 IDAMVQWMKDRHSDTEIQFRPARVLMQDFTGVPGVVDLAAMREAVQAAGKDPAMINPLSP 126
+ A+ W+K+R SD EIQ+RPARVLMQDFTGVP VVDLAAMR A+ AG DP INPLSP
Sbjct: 63 LKAIAAWLKERRSDREIQYRPARVLMQDFTGVPAVVDLAAMRAAMAKAGGDPQRINPLSP 122
Query: 127 VDLVIDHSVMVDKFGDASSFKDNVAIEMERNQERYEFLRWGQQAFDNFRVVPPGTGICHQ 186
VDLVIDHSVMVDK+ AS+F NV IEM+RN ERY FLRWGQ AF+NF VVPPGTGICHQ
Sbjct: 123 VDLVIDHSVMVDKYASASAFGQNVDIEMQRNHERYAFLRWGQSAFNNFSVVPPGTGICHQ 182
Query: 187 VNLEYLGKTVWQKDQDGKTIAYPDTLVGTDSHTTMINGLGILGWGVGGIEAEAAMLGQPV 246
VNLEYLG+TVW KD+DG+T A+PDTLVGTDSHTTMINGLG+LGWGVGGIEAEAAMLGQPV
Sbjct: 183 VNLEYLGRTVWTKDEDGRTYAFPDTLVGTDSHTTMINGLGVLGWGVGGIEAEAAMLGQPV 242
Query: 247 SMLIPEVVGFKITGKLREGITATDLVLTVTEMLRKKGVVGKFVEFYGDGLKDMPVADRAT 306
SMLIPEV+GFK+TGKL+EGITATDLVLTVT+MLRKKGVVGKFVEFYGDGL D+P+ADRAT
Sbjct: 243 SMLIPEVIGFKLTGKLKEGITATDLVLTVTQMLRKKGVVGKFVEFYGDGLADLPLADRAT 302
Query: 307 IANMAPEYGATCGFFPVDEQTIKYMRLTGREEEQLELVEAYAKAQGLWREPGHEPVYTDN 366
IANMAPEYGATCGFFPVDE T++Y+RL+GR + ++LVEAY+K QGLWR PG EPV+TD+
Sbjct: 303 IANMAPEYGATCGFFPVDEVTLEYLRLSGRTPQTVKLVEAYSKTQGLWRLPGKEPVFTDS 362
Query: 367 LELDMGEVEASLAGPKRPQDRVALKNMKSSFELLMETAEGPAENREANLESEGGQ-TAVG 425
L LDMG VEASLAGPKRPQDRV+L N+ +F + P+ E LESEGG AVG
Sbjct: 363 LALDMGSVEASLAGPKRPQDRVSLPNVAQAFTDFLGLQFKPSSKEEGRLESEGGGGVAVG 422
Query: 426 ----VDDSYKHHASQPLEMNGEKSRLDPGAVVIAAITSCTNTSNPSVMMAAGLIAQKAVQ 481
+ ++ HH G RL GAVVIAAITSCTNTSNPSVMMAAGL+A+KAV+
Sbjct: 423 NADLIGEADYHH-------EGSTYRLKNGAVVIAAITSCTNTSNPSVMMAAGLVAKKAVE 475
Query: 482 KGLSTKPWVKTSLAPGSKVVTDYLKVGGFQDDLDKLGFNLVGYGCTTCIGNSGPLPDAVE 541
KGL KPWVK+SLAPGSKVVTDY K G LD+LGF LVGYGCTTCIGNSGPLP+ +E
Sbjct: 476 KGLKRKPWVKSSLAPGSKVVTDYYKAAGLTQYLDELGFALVGYGCTTCIGNSGPLPEPIE 535
Query: 542 KAISDGDLTVASVLSGNRNFEGRVHPLVKTNWLASPPLVVAYALAGNVRLDLSQDPLGND 601
KAI DLTVASVLSGNRNFEGRVHPLVKTNWLASPPLVVAYALAG VR+D+S +PLGND
Sbjct: 536 KAIQKADLTVASVLSGNRNFEGRVHPLVKTNWLASPPLVVAYALAGTVRIDISSEPLGND 595
Query: 602 KDGNPVYLKDLWPSQQEIAEAVEKVKTDMFRKEYAEVFDGDATWKSIKVPESKVYEWSDK 661
KDG+PVYL+D+WPS +EIA+AV +V T MF KEYAEVF GD W++I+VP++ Y W++
Sbjct: 596 KDGHPVYLRDIWPSTKEIADAVTQVNTAMFHKEYAEVFAGDEQWQAIEVPQAATYVWNND 655
Query: 662 STYIQHPPFFEGLKEEPDAIDDIKDANILALLGDSVTTDHISPAGSFKPDTPAGKYLQEH 721
STYIQHPPFF+ + + D++ A +LALLGDSVTTDHISPAG+ K D+PAG YL+E
Sbjct: 656 STYIQHPPFFDDIGGPAPVVKDVEGAKVLALLGDSVTTDHISPAGNIKADSPAGHYLREQ 715
Query: 722 GVEPKDFNSYGSRRGNHEVMMRGTFANVRIRNEMLDGVEGGYTKFVPTGEQMAIYDAAMK 781
GVEP+DFNSYGSRRGNH+VMMRGTFAN+RIRNEML G EGG T ++PTGE++ IYDAAM+
Sbjct: 716 GVEPRDFNSYGSRRGNHQVMMRGTFANIRIRNEMLGGEEGGNTIYIPTGEKLPIYDAAMR 775
Query: 782 YQEKGTPLVVIAGKEYGTGSSRDWAAKGTRLLGVKAVVAESYERIHRSNLIGMGVMPLQF 841
YQ GTPLVVIAG+EYGTGSSRDWAAKGT LLGVKAV+AES+ERIHRSNL+GMGV+PLQF
Sbjct: 776 YQASGTPLVVIAGQEYGTGSSRDWAAKGTNLLGVKAVIAESFERIHRSNLVGMGVLPLQF 835
Query: 842 PEGTDRKSLKLTGEETISIEGLSG-EIKPGQTLKMTVKYKDGSTETCELKSRIDTANEAV 900
+RKSL LTG+ET+ I GL+G E+ P L + V +DG+TE E+ RIDT NE
Sbjct: 836 KLDQNRKSLNLTGKETLDILGLTGVELTPRMNLTLVVTREDGNTEKVEVLCRIDTLNEVE 895
Query: 901 YFKHGGILHYVVREML 916
YFK GGILHYV+R+++
Sbjct: 896 YFKAGGILHYVLRQLI 911
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: 2370
Number of extensions: 104
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: 919
Length of database: 913
Length adjustment: 43
Effective length of query: 876
Effective length of database: 870
Effective search space: 762120
Effective search space used: 762120
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 Pf1N1B4_3888 (Aconitate hydratase (EC 4.2.1.3))
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.9531.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 1420.5 0.0 0 1420.2 0.0 1.0 1 lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3888 Aconitate hydratase (EC 4.2.1.3)
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3888 Aconitate hydratase (EC 4.2.1.3)
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1420.2 0.0 0 0 1 876 [] 18 911 .. 18 911 .. 0.97
Alignments for each domain:
== domain 1 score: 1420.2 bits; conditional E-value: 0
TIGR01341 1 kkvyyyslkaleeslekisklpkslrillesvlrnldgskikeedveallkwkkeelkdeeiaf 64
k+++y+sl+++++sl++++klp sl++lle++lr+ d+++++ d++a++ w ke +d+ei++
lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3888 18 KTYHYFSLPEAAKSLGDLDKLPMSLKVLLENLLRWEDEKTVTGADLKAIAAWLKERRSDREIQY 81
689************************************************************* PP
TIGR01341 65 kparvvlqdftGvpavvdlaalreavknlgkdpekinplvpvdlvidhsvqvdkageeealean 128
+parv++qdftGvpavvdlaa+r a+++ g+dp++inpl+pvdlvidhsv vdk+ + +a+ +n
lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3888 82 RPARVLMQDFTGVPAVVDLAAMRAAMAKAGGDPQRINPLSPVDLVIDHSVMVDKYASASAFGQN 145
**************************************************************** PP
TIGR01341 129 velefernkerykflkwakkafknlkvvppgtGivhqvnleylakvvfeaekdgellaypdslv 192
v++e++rn+ery+fl+w++ af+n++vvppgtGi+hqvnleyl++ v+++++dg+++a+pd+lv
lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3888 146 VDIEMQRNHERYAFLRWGQSAFNNFSVVPPGTGICHQVNLEYLGRTVWTKDEDGRTYAFPDTLV 209
**************************************************************** PP
TIGR01341 193 GtdshttminGlGvlGwGvGGieaeaallGqpvslsvpeviGvkltGklreGvtatdlvltvte 256
GtdshttminGlGvlGwGvGGieaeaa+lGqpvs+ +peviG+kltGkl+eG+tatdlvltvt+
lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3888 210 GTDSHTTMINGLGVLGWGVGGIEAEAAMLGQPVSMLIPEVIGFKLTGKLKEGITATDLVLTVTQ 273
**************************************************************** PP
TIGR01341 257 llrkkgvvgkfveffGeglkelsladratianmapeyGataaffpiddvtlqylrltgrdedkv 320
+lrkkgvvgkfvef+G+gl+ l+ladratianmapeyGat++ffp+d+vtl+ylrl+gr ++v
lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3888 274 MLRKKGVVGKFVEFYGDGLADLPLADRATIANMAPEYGATCGFFPVDEVTLEYLRLSGRTPQTV 337
**************************************************************** PP
TIGR01341 321 elvekylkaqelfvddseepkytdvveldlsdveasvaGpkrpqdrvalkevkaafkss..les 382
+lve+y k+q+l++ ++ep++td + ld+ +veas+aGpkrpqdrv+l +v +af+ l+
lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3888 338 KLVEAYSKTQGLWRLPGKEPVFTDSLALDMGSVEASLAGPKRPQDRVSLPNVAQAFTDFlgLQF 401
********************************************************99844444 PP
TIGR01341 383 nagekg.lalr..............keakekklegkeaelkdgavviaaitsctntsnpsvllg 431
+ ++k+ l+ +++ eg++++lk+gavviaaitsctntsnpsv+++
lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3888 402 KPSSKEeGRLEseggggvavgnadlIGEADYHHEGSTYRLKNGAVVIAAITSCTNTSNPSVMMA 465
4444430334466677766666655344566668****************************** PP
TIGR01341 432 agllakkavelGlkvkpyvktslapGskvvtdylaesgllpyleelGfnlvGyGcttciGnsGp 495
agl+akkave Glk+kp+vk+slapGskvvtdy + +gl++yl+elGf lvGyGcttciGnsGp
lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3888 466 AGLVAKKAVEKGLKRKPWVKSSLAPGSKVVTDYYKAAGLTQYLDELGFALVGYGCTTCIGNSGP 529
**************************************************************** PP
TIGR01341 496 leeeveeaikendlevsavlsGnrnfegrihplvkanylaspplvvayalaGtvdidlekepig 559
l+e +e+ai++ dl+v++vlsGnrnfegr+hplvk+n+laspplvvayalaGtv id+++ep+g
lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3888 530 LPEPIEKAIQKADLTVASVLSGNRNFEGRVHPLVKTNWLASPPLVVAYALAGTVRIDISSEPLG 593
**************************************************************** PP
TIGR01341 560 tdkdGkkvylkdiwpsakeiaelvkkavkkelfkkeyeevtegnerwnelevtssdlyewdeks 623
dkdG++vyl+diwps+keia++v ++v++ +f+key+ev+ g+e+w+ +ev++ ++y w+++s
lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3888 594 NDKDGHPVYLRDIWPSTKEIADAV-TQVNTAMFHKEYAEVFAGDEQWQAIEVPQAATYVWNNDS 656
**********************65.689************************************ PP
TIGR01341 624 tyireppffeelklepeevedikgarillllGdsittdhispaGsikkdspaakylkekGverr 687
tyi++ppff+++ v+d++ga++l+llGds+ttdhispaG+ik dspa++yl+e+Gve+r
lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3888 657 TYIQHPPFFDDIGGPAPVVKDVEGAKVLALLGDSVTTDHISPAGNIKADSPAGHYLREQGVEPR 720
*************988999********************************************* PP
TIGR01341 688 dfnsyGsrrGnhevmlrGtfaniriknklvkgkeGgltvylpdsevvsvydaamkykkegvplv 751
dfnsyGsrrGnh+vm+rGtfaniri+n+++ g+eGg t+y+p++e++ +ydaam+y+ +g+plv
lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3888 721 DFNSYGSRRGNHQVMMRGTFANIRIRNEMLGGEEGGNTIYIPTGEKLPIYDAAMRYQASGTPLV 784
**************************************************************** PP
TIGR01341 752 vlaGkeyGsGssrdwaakgtkllGvkaviaesferihrsnlvgmGvlplefkqgedaetlgltg 815
v+aG+eyG+Gssrdwaakgt+llGvkaviaesferihrsnlvgmGvlpl+fk +++++l+ltg
lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3888 785 VIAGQEYGTGSSRDWAAKGTNLLGVKAVIAESFERIHRSNLVGMGVLPLQFKLDQNRKSLNLTG 848
**************************************************************** PP
TIGR01341 816 eetidvddie..elkpkkevtvelvkedgeketveavlridtevelayvkkgGilqyvlrkll 876
+et+d+ +++ el p+ ++t+++++edg+ e ve+ +ridt e++y+k gGil+yvlr+l+
lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3888 849 KETLDILGLTgvELTPRMNLTLVVTREDGNTEKVEVLCRIDTLNEVEYFKAGGILHYVLRQLI 911
******998633688*********************************************975 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (876 nodes)
Target sequences: 1 (913 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: 0.06u 0.03s 00:00:00.09 Elapsed: 00:00:00.08
# Mc/sec: 8.96
//
[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