Align Aconitate hydratase (EC 4.2.1.3) (characterized)
to candidate PfGW456L13_4052 Aconitate hydratase (EC 4.2.1.3)
Query= reanno::Marino:GFF3491
(919 letters)
>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4052
Length = 913
Score = 1315 bits (3404), Expect = 0.0
Identities = 653/912 (71%), Positives = 749/912 (82%), Gaps = 5/912 (0%)
Query: 7 SKDSLNTLSSLDAGGKTFHYYSLPKAADTLGDLNRLPFSLKVLMENLLRNEDGTTVDRSH 66
S DSLNTL +L G KT+HY+SLP+AA +LGDLN+LP SLKVL+ENLLR ED TV +
Sbjct: 3 SLDSLNTLKTLQVGNKTYHYFSLPEAAKSLGDLNKLPMSLKVLLENLLRWEDEKTVTGAD 62
Query: 67 IDAMVQWMKDRHSDTEIQFRPARVLMQDFTGVPGVVDLAAMREAVQAAGKDPAMINPLSP 126
+ A+ W+K+R SD EIQ+RPARVLMQDFTGVP VVDLAAMR A+ AG +P INPLSP
Sbjct: 63 LKALAAWLKERRSDREIQYRPARVLMQDFTGVPAVVDLAAMRAAMAKAGGNPQRINPLSP 122
Query: 127 VDLVIDHSVMVDKFGDASSFKDNVAIEMERNQERYEFLRWGQQAFDNFRVVPPGTGICHQ 186
VDLVIDHSVMVDKF +S+F+ NV IEM+RN ERY FLRWGQ AFDNF VVPPGTGICHQ
Sbjct: 123 VDLVIDHSVMVDKFASSSAFEQNVDIEMQRNGERYAFLRWGQSAFDNFSVVPPGTGICHQ 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
IANMAPEYGATCGFFPVD+ T+ Y+RL+GR E ++LVEAY+KAQGLWR PG EPV+TD+
Sbjct: 303 IANMAPEYGATCGFFPVDDITLDYLRLSGRPLETVQLVEAYSKAQGLWRLPGQEPVFTDS 362
Query: 367 LELDMGEVEASLAGPKRPQDRVALKNMKSSFELLMETAEGPAENREANLESEGGQ-TAVG 425
L LDMG VEA LAGPKRPQDRV L N+ +F + P E LESEGG AVG
Sbjct: 363 LALDMGSVEACLAGPKRPQDRVTLPNVAQAFSDFTDLQFKPTSKEEGRLESEGGGGVAVG 422
Query: 426 VDDSYKHHASQPLEMNGEKSRLDPGAVVIAAITSCTNTSNPSVMMAAGLIAQKAVQKGLS 485
D + G+ RL GAVVIAAITSCTNTSNPSVMMAAGL+A+KAV+KGL
Sbjct: 423 NADMA---GEADYDYEGQTYRLKNGAVVIAAITSCTNTSNPSVMMAAGLVAKKAVEKGLK 479
Query: 486 TKPWVKTSLAPGSKVVTDYLKVGGFQDDLDKLGFNLVGYGCTTCIGNSGPLPDAVEKAIS 545
KPWVK+SLAPGSKVVTDY K G LD+LGF LVGYGCTTCIGNSGPL + +EKAI
Sbjct: 480 RKPWVKSSLAPGSKVVTDYYKAAGLTQYLDELGFALVGYGCTTCIGNSGPLSEPIEKAIQ 539
Query: 546 DGDLTVASVLSGNRNFEGRVHPLVKTNWLASPPLVVAYALAGNVRLDLSQDPLGNDKDGN 605
DLTVASVLSGNRNFEGRVHPLVKTNWLASPPLVVAYALAG VR DLS++PLG+ KDG
Sbjct: 540 QADLTVASVLSGNRNFEGRVHPLVKTNWLASPPLVVAYALAGTVRTDLSREPLGDGKDGK 599
Query: 606 PVYLKDLWPSQQEIAEAVEKVKTDMFRKEYAEVFDGDATWKSIKVPESKVYEWSDKSTYI 665
PVYL+D+WPS +EIA+AV +V T MF KEYAEVF GD W++IKVP++ Y W D STYI
Sbjct: 600 PVYLRDIWPSSKEIADAVNQVNTAMFHKEYAEVFAGDEQWQAIKVPQAATYVWQDDSTYI 659
Query: 666 QHPPFFEGLKEEPDAIDDIKDANILALLGDSVTTDHISPAGSFKPDTPAGKYLQEHGVEP 725
QHPPFF+ + + D+ A ILALLGDSVTTDHISPAG+ K D+PAG+YL++ GVEP
Sbjct: 660 QHPPFFDDIGGPAPVVKDVSGARILALLGDSVTTDHISPAGNIKVDSPAGQYLRDKGVEP 719
Query: 726 KDFNSYGSRRGNHEVMMRGTFANVRIRNEMLDGVEGGYTKFVPTGEQMAIYDAAMKYQEK 785
+DFNSYGSRRGNHEVMMRGTFAN+RIRNEML G EGG T+++PTGE+M+IYDAAM+YQ
Sbjct: 720 RDFNSYGSRRGNHEVMMRGTFANIRIRNEMLGGEEGGNTRYIPTGEKMSIYDAAMRYQAS 779
Query: 786 GTPLVVIAGKEYGTGSSRDWAAKGTRLLGVKAVVAESYERIHRSNLIGMGVMPLQFPEGT 845
GTPLVVIAG+EYGTGSSRDWAAKGT LLGVKAVVAES+ERIHRSNL+GMGV+PLQF
Sbjct: 780 GTPLVVIAGQEYGTGSSRDWAAKGTILLGVKAVVAESFERIHRSNLVGMGVLPLQFKLDQ 839
Query: 846 DRKSLKLTGEETISIEGLSG-EIKPGQTLKMTVKYKDGSTETCELKSRIDTANEAVYFKH 904
+RKSLKL G ET+ I GL+G E+ P L + + +DGS E E+ RIDT NE YFK
Sbjct: 840 NRKSLKLGGSETLDILGLTGVELTPRMNLTLVITREDGSREKIEVLCRIDTLNEVEYFKS 899
Query: 905 GGILHYVVREML 916
GGILHYV+R+++
Sbjct: 900 GGILHYVLRQLI 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: 2329
Number of extensions: 104
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: 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 PfGW456L13_4052 (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.13139.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 1416.8 0.0 0 1416.6 0.0 1.0 1 lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4052 Aconitate hydratase (EC 4.2.1.3)
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4052 Aconitate hydratase (EC 4.2.1.3)
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1416.6 0.0 0 0 1 876 [] 18 911 .. 18 911 .. 0.97
Alignments for each domain:
== domain 1 score: 1416.6 bits; conditional E-value: 0
TIGR01341 1 kkvyyyslkaleeslekisklpkslrillesvlrnldgskikeedveallkwkke 55
k+++y+sl+++++sl++++klp sl++lle++lr+ d+++++ d++al+ w ke
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4052 18 KTYHYFSLPEAAKSLGDLNKLPMSLKVLLENLLRWEDEKTVTGADLKALAAWLKE 72
689**************************************************** PP
TIGR01341 56 elkdeeiafkparvvlqdftGvpavvdlaalreavknlgkdpekinplvpvdlvi 110
+d+ei+++parv++qdftGvpavvdlaa+r a+++ g++p++inpl+pvdlvi
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4052 73 RRSDREIQYRPARVLMQDFTGVPAVVDLAAMRAAMAKAGGNPQRINPLSPVDLVI 127
******************************************************* PP
TIGR01341 111 dhsvqvdkageeealeanvelefernkerykflkwakkafknlkvvppgtGivhq 165
dhsv vdk+ +++a+e+nv++e++rn ery+fl+w++ af n++vvppgtGi+hq
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4052 128 DHSVMVDKFASSSAFEQNVDIEMQRNGERYAFLRWGQSAFDNFSVVPPGTGICHQ 182
******************************************************* PP
TIGR01341 166 vnleylakvvfeaekdgellaypdslvGtdshttminGlGvlGwGvGGieaeaal 220
vnleyl++ v+++++dg+++a+pd+lvGtdshttminGlGvlGwGvGGieaeaa+
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4052 183 VNLEYLGRTVWTKDEDGRTYAFPDTLVGTDSHTTMINGLGVLGWGVGGIEAEAAM 237
******************************************************* PP
TIGR01341 221 lGqpvslsvpeviGvkltGklreGvtatdlvltvtellrkkgvvgkfveffGegl 275
lGqpvs+ +peviG+kltGkl+eG+tatdlvltvt++lrkkgvvgkfvef+G+gl
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4052 238 LGQPVSMLIPEVIGFKLTGKLKEGITATDLVLTVTQMLRKKGVVGKFVEFYGDGL 292
******************************************************* PP
TIGR01341 276 kelsladratianmapeyGataaffpiddvtlqylrltgrdedkvelvekylkaq 330
+ l+ladratianmapeyGat++ffp+dd tl+ylrl+gr+ ++v+lve+y kaq
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4052 293 ADLPLADRATIANMAPEYGATCGFFPVDDITLDYLRLSGRPLETVQLVEAYSKAQ 347
******************************************************* PP
TIGR01341 331 elfvddseepkytdvveldlsdveasvaGpkrpqdrvalkevkaafkss..lesn 383
+l++ ++ep++td + ld+ +vea++aGpkrpqdrv+l +v +af l+ +
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4052 348 GLWRLPGQEPVFTDSLALDMGSVEACLAGPKRPQDRVTLPNVAQAFSDFtdLQFK 402
*********************************************9976456666 PP
TIGR01341 384 agekgla.lr..............keakekklegkeaelkdgavviaaitsctnt 423
++k+ + l+ ++ eg++++lk+gavviaaitsctnt
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4052 403 PTSKEEGrLEseggggvavgnadmAGEADYDYEGQTYRLKNGAVVIAAITSCTNT 457
666554313366777777766655445566778********************** PP
TIGR01341 424 snpsvllgagllakkavelGlkvkpyvktslapGskvvtdylaesgllpyleelG 478
snpsv+++agl+akkave Glk+kp+vk+slapGskvvtdy + +gl++yl+elG
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4052 458 SNPSVMMAAGLVAKKAVEKGLKRKPWVKSSLAPGSKVVTDYYKAAGLTQYLDELG 512
******************************************************* PP
TIGR01341 479 fnlvGyGcttciGnsGpleeeveeaikendlevsavlsGnrnfegrihplvkany 533
f lvGyGcttciGnsGpl+e +e+ai++ dl+v++vlsGnrnfegr+hplvk+n+
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4052 513 FALVGYGCTTCIGNSGPLSEPIEKAIQQADLTVASVLSGNRNFEGRVHPLVKTNW 567
******************************************************* PP
TIGR01341 534 laspplvvayalaGtvdidlekepigtdkdGkkvylkdiwpsakeiaelvkkavk 588
laspplvvayalaGtv dl++ep+g +kdGk+vyl+diwps keia++v+ +v+
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4052 568 LASPPLVVAYALAGTVRTDLSREPLGDGKDGKPVYLRDIWPSSKEIADAVN-QVN 621
************************************************775.79* PP
TIGR01341 589 kelfkkeyeevtegnerwnelevtssdlyewdekstyireppffeelklepeeve 643
+ +f+key+ev+ g+e+w+ ++v++ ++y w+++styi++ppff+++ v+
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4052 622 TAMFHKEYAEVFAGDEQWQAIKVPQAATYVWQDDSTYIQHPPFFDDIGGPAPVVK 676
************************************************988999* PP
TIGR01341 644 dikgarillllGdsittdhispaGsikkdspaakylkekGverrdfnsyGsrrGn 698
d+ garil+llGds+ttdhispaG+ik dspa++yl++kGve+rdfnsyGsrrGn
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4052 677 DVSGARILALLGDSVTTDHISPAGNIKVDSPAGQYLRDKGVEPRDFNSYGSRRGN 731
******************************************************* PP
TIGR01341 699 hevmlrGtfaniriknklvkgkeGgltvylpdsevvsvydaamkykkegvplvvl 753
hevm+rGtfaniri+n+++ g+eGg t+y+p++e++s+ydaam+y+ +g+plvv+
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4052 732 HEVMMRGTFANIRIRNEMLGGEEGGNTRYIPTGEKMSIYDAAMRYQASGTPLVVI 786
******************************************************* PP
TIGR01341 754 aGkeyGsGssrdwaakgtkllGvkaviaesferihrsnlvgmGvlplefkqgeda 808
aG+eyG+Gssrdwaakgt llGvkav+aesferihrsnlvgmGvlpl+fk +++
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4052 787 AGQEYGTGSSRDWAAKGTILLGVKAVVAESFERIHRSNLVGMGVLPLQFKLDQNR 841
******************************************************* PP
TIGR01341 809 etlgltgeetidvddie..elkpkkevtvelvkedgeketveavlridtevelay 861
++l l g+et+d+ +++ el p+ ++t+++++edg++e +e+ +ridt e++y
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4052 842 KSLKLGGSETLDILGLTgvELTPRMNLTLVITREDGSREKIEVLCRIDTLNEVEY 896
*************998633688********************************* PP
TIGR01341 862 vkkgGilqyvlrkll 876
+k+gGil+yvlr+l+
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4052 897 FKSGGILHYVLRQLI 911
************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: 0.07u 0.03s 00:00:00.10 Elapsed: 00:00:00.09
# Mc/sec: 8.26
//
[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