Align Aconitate hydratase (EC 4.2.1.3) (characterized)
to candidate Pf6N2E2_2301 Aconitate hydratase (EC 4.2.1.3)
Query= reanno::Marino:GFF3491
(919 letters)
>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2301
Length = 913
Score = 1322 bits (3421), Expect = 0.0
Identities = 653/912 (71%), Positives = 751/912 (82%), Gaps = 5/912 (0%)
Query: 7 SKDSLNTLSSLDAGGKTFHYYSLPKAADTLGDLNRLPFSLKVLMENLLRNEDGTTVDRSH 66
S DSL TL +L +T+HY+SLP+AA +LGDL++LP SLKVL+ENLLR ED TV +
Sbjct: 3 SLDSLKTLKTLQVDARTYHYFSLPEAARSLGDLDKLPMSLKVLLENLLRWEDEKTVTGTD 62
Query: 67 IDAMVQWMKDRHSDTEIQFRPARVLMQDFTGVPGVVDLAAMREAVQAAGKDPAMINPLSP 126
+ A+ W+K+R SD EIQ+RPARVLMQDFTGVP VVDLAAMR AV+ AG DP INPLSP
Sbjct: 63 LKALAGWLKERRSDREIQYRPARVLMQDFTGVPAVVDLAAMRAAVEKAGGDPQRINPLSP 122
Query: 127 VDLVIDHSVMVDKFGDASSFKDNVAIEMERNQERYEFLRWGQQAFDNFRVVPPGTGICHQ 186
VDLVIDHSVMVDKF + +F+ NV IEM+RN ERY FLRWGQ AFDNF VVPPGTGICHQ
Sbjct: 123 VDLVIDHSVMVDKFASSQAFEQNVDIEMQRNGERYAFLRWGQSAFDNFSVVPPGTGICHQ 182
Query: 187 VNLEYLGKTVWQKDQDGKTIAYPDTLVGTDSHTTMINGLGILGWGVGGIEAEAAMLGQPV 246
VNLEYLG+TVW K++DG+T A+PDTLVGTDSHTTMINGLG+LGWGVGGIEAEAAMLGQPV
Sbjct: 183 VNLEYLGRTVWTKEEDGRTYAFPDTLVGTDSHTTMINGLGVLGWGVGGIEAEAAMLGQPV 242
Query: 247 SMLIPEVVGFKITGKLREGITATDLVLTVTEMLRKKGVVGKFVEFYGDGLKDMPVADRAT 306
SMLIPEV+GFK+TGKLREGITATDLVLTVT+MLRKKGVVGKFVEFYGDGL D+P+ADRAT
Sbjct: 243 SMLIPEVIGFKLTGKLREGITATDLVLTVTQMLRKKGVVGKFVEFYGDGLADLPLADRAT 302
Query: 307 IANMAPEYGATCGFFPVDEQTIKYMRLTGREEEQLELVEAYAKAQGLWREPGHEPVYTDN 366
IANMAPEYGATCGFFPVDE T+ Y+RL+GR E ++LVEAY KAQGLWR PG EPV+TD
Sbjct: 303 IANMAPEYGATCGFFPVDEVTLDYLRLSGRPAETVKLVEAYCKAQGLWRLPGQEPVFTDT 362
Query: 367 LELDMGEVEASLAGPKRPQDRVALKNMKSSFELLMETAEGPAENREANLESEGGQ-TAVG 425
LELDMG VEASLAGPKRPQDRV+L N+ +F + P E LESEGG AVG
Sbjct: 363 LELDMGSVEASLAGPKRPQDRVSLPNVGQAFSDFLGLQVKPTSKEEGRLESEGGGGVAVG 422
Query: 426 VDDSYKHHASQPLEMNGEKSRLDPGAVVIAAITSCTNTSNPSVMMAAGLIAQKAVQKGLS 485
D E G RL GAVVIAAITSCTNTSNPSVMMAAGL+A+KAV+KGL+
Sbjct: 423 NADQV---GEAEYEFEGHTHRLKNGAVVIAAITSCTNTSNPSVMMAAGLLAKKAVEKGLT 479
Query: 486 TKPWVKTSLAPGSKVVTDYLKVGGFQDDLDKLGFNLVGYGCTTCIGNSGPLPDAVEKAIS 545
KPWVK+SLAPGSKVVTDY K G + LDKLGF+LVGYGCTTCIGNSGPLP+ +EKAI
Sbjct: 480 RKPWVKSSLAPGSKVVTDYYKAAGLTEYLDKLGFDLVGYGCTTCIGNSGPLPEPIEKAIQ 539
Query: 546 DGDLTVASVLSGNRNFEGRVHPLVKTNWLASPPLVVAYALAGNVRLDLSQDPLGNDKDGN 605
DLTVASVLSGNRNFEGRVHPLVKTNWLASPPLVVAYALAG VR+D+S +PLGND+DG
Sbjct: 540 KADLTVASVLSGNRNFEGRVHPLVKTNWLASPPLVVAYALAGTVRIDISSEPLGNDRDGK 599
Query: 606 PVYLKDLWPSQQEIAEAVEKVKTDMFRKEYAEVFDGDATWKSIKVPESKVYEWSDKSTYI 665
PVYL+D+WPS QE+A AV +V T MF KEYA VF GD W++I+VP++ Y W D STYI
Sbjct: 600 PVYLRDVWPSSQEVATAVAQVNTSMFHKEYAAVFAGDEQWQAIEVPQAATYVWQDDSTYI 659
Query: 666 QHPPFFEGLKEEPDAIDDIKDANILALLGDSVTTDHISPAGSFKPDTPAGKYLQEHGVEP 725
QHPPFF+ + P A+ +++ A ILALLGDSVTTDHISPAG+ K D+PAG+YL+E GVEP
Sbjct: 660 QHPPFFDAIDGPPPAVKNVEGARILALLGDSVTTDHISPAGNIKADSPAGRYLREQGVEP 719
Query: 726 KDFNSYGSRRGNHEVMMRGTFANVRIRNEMLDGVEGGYTKFVPTGEQMAIYDAAMKYQEK 785
+DFNSYGSRRGNH+VMMRGTFAN+RIRNEMLDG EGG T ++P+GE+M IYDAAM YQ
Sbjct: 720 RDFNSYGSRRGNHQVMMRGTFANIRIRNEMLDGEEGGNTIYIPSGERMPIYDAAMLYQAV 779
Query: 786 GTPLVVIAGKEYGTGSSRDWAAKGTRLLGVKAVVAESYERIHRSNLIGMGVMPLQFPEGT 845
GTPLVVIAG+EYGTGSSRDWAAKGT LLGVKAV+AES+ERIHRSNL+GMGV+PLQF
Sbjct: 780 GTPLVVIAGQEYGTGSSRDWAAKGTNLLGVKAVIAESFERIHRSNLVGMGVLPLQFKLDQ 839
Query: 846 DRKSLKLTGEETISIEGLSG-EIKPGQTLKMTVKYKDGSTETCELKSRIDTANEAVYFKH 904
+RKSL LTG+ET+ I GL+ E+ P L + + +DGS E E+ RIDT NE YFK
Sbjct: 840 NRKSLNLTGKETLDILGLNDVELTPRMNLPLVITREDGSQERIEVLCRIDTLNEVEYFKA 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: 2341
Number of extensions: 98
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 Pf6N2E2_2301 (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.2286.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 1426.4 0.0 0 1426.2 0.0 1.0 1 lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2301 Aconitate hydratase (EC 4.2.1.3)
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2301 Aconitate hydratase (EC 4.2.1.3)
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1426.2 0.0 0 0 2 876 .] 19 911 .. 18 911 .. 0.97
Alignments for each domain:
== domain 1 score: 1426.2 bits; conditional E-value: 0
TIGR01341 2 kvyyyslkaleeslekisklpkslrillesvlrnldgskikeedveallkwkkeelkdeeiafk 65
+++y+sl++++ sl++++klp sl++lle++lr+ d+++++ d++al+ w ke +d+ei+++
lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2301 19 TYHYFSLPEAARSLGDLDKLPMSLKVLLENLLRWEDEKTVTGTDLKALAGWLKERRSDREIQYR 82
79************************************************************** PP
TIGR01341 66 parvvlqdftGvpavvdlaalreavknlgkdpekinplvpvdlvidhsvqvdkageeealeanv 129
parv++qdftGvpavvdlaa+r av++ g+dp++inpl+pvdlvidhsv vdk+ +++a+e+nv
lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2301 83 PARVLMQDFTGVPAVVDLAAMRAAVEKAGGDPQRINPLSPVDLVIDHSVMVDKFASSQAFEQNV 146
**************************************************************** PP
TIGR01341 130 elefernkerykflkwakkafknlkvvppgtGivhqvnleylakvvfeaekdgellaypdslvG 193
++e++rn ery+fl+w++ af n++vvppgtGi+hqvnleyl++ v+++e+dg+++a+pd+lvG
lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2301 147 DIEMQRNGERYAFLRWGQSAFDNFSVVPPGTGICHQVNLEYLGRTVWTKEEDGRTYAFPDTLVG 210
**************************************************************** PP
TIGR01341 194 tdshttminGlGvlGwGvGGieaeaallGqpvslsvpeviGvkltGklreGvtatdlvltvtel 257
tdshttminGlGvlGwGvGGieaeaa+lGqpvs+ +peviG+kltGklreG+tatdlvltvt++
lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2301 211 TDSHTTMINGLGVLGWGVGGIEAEAAMLGQPVSMLIPEVIGFKLTGKLREGITATDLVLTVTQM 274
**************************************************************** PP
TIGR01341 258 lrkkgvvgkfveffGeglkelsladratianmapeyGataaffpiddvtlqylrltgrdedkve 321
lrkkgvvgkfvef+G+gl+ l+ladratianmapeyGat++ffp+d+vtl+ylrl+gr+ ++v+
lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2301 275 LRKKGVVGKFVEFYGDGLADLPLADRATIANMAPEYGATCGFFPVDEVTLDYLRLSGRPAETVK 338
**************************************************************** PP
TIGR01341 322 lvekylkaqelfvddseepkytdvveldlsdveasvaGpkrpqdrvalkevkaafkss..lesn 383
lve+y+kaq+l++ ++ep++td++eld+ +veas+aGpkrpqdrv+l +v +af l+++
lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2301 339 LVEAYCKAQGLWRLPGQEPVFTDTLELDMGSVEASLAGPKRPQDRVSLPNVGQAFSDFlgLQVK 402
*******************************************************998445666 PP
TIGR01341 384 agekgla.lr..............keakekklegkeaelkdgavviaaitsctntsnpsvllga 432
++k+ + l+ e+ +eg++++lk+gavviaaitsctntsnpsv+++a
lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2301 403 PTSKEEGrLEseggggvavgnadqVGEAEYEFEGHTHRLKNGAVVIAAITSCTNTSNPSVMMAA 466
566654314477788887877754345577889******************************* PP
TIGR01341 433 gllakkavelGlkvkpyvktslapGskvvtdylaesgllpyleelGfnlvGyGcttciGnsGpl 496
gllakkave Gl +kp+vk+slapGskvvtdy + +gl++yl++lGf+lvGyGcttciGnsGpl
lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2301 467 GLLAKKAVEKGLTRKPWVKSSLAPGSKVVTDYYKAAGLTEYLDKLGFDLVGYGCTTCIGNSGPL 530
**************************************************************** PP
TIGR01341 497 eeeveeaikendlevsavlsGnrnfegrihplvkanylaspplvvayalaGtvdidlekepigt 560
+e +e+ai++ dl+v++vlsGnrnfegr+hplvk+n+laspplvvayalaGtv id+++ep+g
lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2301 531 PEPIEKAIQKADLTVASVLSGNRNFEGRVHPLVKTNWLASPPLVVAYALAGTVRIDISSEPLGN 594
**************************************************************** PP
TIGR01341 561 dkdGkkvylkdiwpsakeiaelvkkavkkelfkkeyeevtegnerwnelevtssdlyewdekst 624
d+dGk+vyl+d+wps +e+a++v +v++ +f+key++v+ g+e+w+ +ev++ ++y w+++st
lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2301 595 DRDGKPVYLRDVWPSSQEVATAV-AQVNTSMFHKEYAAVFAGDEQWQAIEVPQAATYVWQDDST 657
********************955.689************************************* PP
TIGR01341 625 yireppffeelklepeevedikgarillllGdsittdhispaGsikkdspaakylkekGverrd 688
yi++ppff+ + p v++++garil+llGds+ttdhispaG+ik dspa++yl+e+Gve+rd
lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2301 658 YIQHPPFFDAIDGPPPAVKNVEGARILALLGDSVTTDHISPAGNIKADSPAGRYLREQGVEPRD 721
**************************************************************** PP
TIGR01341 689 fnsyGsrrGnhevmlrGtfaniriknklvkgkeGgltvylpdsevvsvydaamkykkegvplvv 752
fnsyGsrrGnh+vm+rGtfaniri+n++++g+eGg t+y+p +e + +ydaam y+ g+plvv
lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2301 722 FNSYGSRRGNHQVMMRGTFANIRIRNEMLDGEEGGNTIYIPSGERMPIYDAAMLYQAVGTPLVV 785
**************************************************************** PP
TIGR01341 753 laGkeyGsGssrdwaakgtkllGvkaviaesferihrsnlvgmGvlplefkqgedaetlgltge 816
+aG+eyG+Gssrdwaakgt+llGvkaviaesferihrsnlvgmGvlpl+fk +++++l+ltg+
lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2301 786 IAGQEYGTGSSRDWAAKGTNLLGVKAVIAESFERIHRSNLVGMGVLPLQFKLDQNRKSLNLTGK 849
**************************************************************** PP
TIGR01341 817 etidvddieel..kpkkevtvelvkedgeketveavlridtevelayvkkgGilqyvlrkll 876
et+d+ +++++ p+ ++++++++edg++e +e+ +ridt e++y+k gGil+yvlr+l+
lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2301 850 ETLDILGLNDVelTPRMNLPLVITREDGSQERIEVLCRIDTLNEVEYFKAGGILHYVLRQLI 911
*****999875227*********************************************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: 0.05u 0.02s 00:00:00.07 Elapsed: 00:00:00.06
# Mc/sec: 12.53
//
[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