Align Aconitate hydratase (EC 4.2.1.3) (characterized)
to candidate PP_2112 PP_2112 aconitate hydratase 1
Query= reanno::Marino:GFF3491
(919 letters)
>FitnessBrowser__Putida:PP_2112
Length = 913
Score = 1308 bits (3386), Expect = 0.0
Identities = 653/917 (71%), Positives = 748/917 (81%), Gaps = 15/917 (1%)
Query: 7 SKDSLNTLSSLDAGGKTFHYYSLPKAADTLGDLNRLPFSLKVLMENLLRNEDGTTVDRSH 66
S DSLNTL L G KT+HY+SL +AA LGDL RLP SLKVL+ENLLR EDG TV
Sbjct: 3 SLDSLNTLKPLKVGDKTYHYFSLTEAARQLGDLQRLPMSLKVLLENLLRWEDGATVTGDD 62
Query: 67 IDAMVQWMKDRHSDTEIQFRPARVLMQDFTGVPGVVDLAAMREAVQAAGKDPAMINPLSP 126
+ A+ QW+ +R SD EIQ+RPARVLMQDFTGVP VVDLAAMR A+ AG DP INPLSP
Sbjct: 63 LRAIAQWLGERRSDREIQYRPARVLMQDFTGVPAVVDLAAMRAAMAKAGGDPQRINPLSP 122
Query: 127 VDLVIDHSVMVDKFGDASSFKDNVAIEMERNQERYEFLRWGQQAFDNFRVVPPGTGICHQ 186
VDLVIDHSVMVD++G +F +NV IEM+RN ERY FLRWGQ AFDNFRVVPPGTGICHQ
Sbjct: 123 VDLVIDHSVMVDRYGTPQAFAENVDIEMQRNGERYAFLRWGQSAFDNFRVVPPGTGICHQ 182
Query: 187 VNLEYLGKTVWQKDQDGKTIAYPDTLVGTDSHTTMINGLGILGWGVGGIEAEAAMLGQPV 246
VNLEYLG+TVW ++ DG+T A+PDTLVGTDSHTTMINGLG+LGWGVGGIEAEAAMLGQPV
Sbjct: 183 VNLEYLGRTVWTREADGRTYAFPDTLVGTDSHTTMINGLGVLGWGVGGIEAEAAMLGQPV 242
Query: 247 SMLIPEVVGFKITGKLREGITATDLVLTVTEMLRKKGVVGKFVEFYGDGLKDMPVADRAT 306
SMLIPEV+GFK+TGKLREGITATDLVLTVT+MLRKKGVVGKFVEFYGDGL ++P+ADRAT
Sbjct: 243 SMLIPEVIGFKLTGKLREGITATDLVLTVTQMLRKKGVVGKFVEFYGDGLAELPLADRAT 302
Query: 307 IANMAPEYGATCGFFPVDEQTIKYMRLTGREEEQLELVEAYAKAQGLWREPGHEPVYTDN 366
IANMAPEYGATCGFFPVD+ T+ Y+RL+GR E ++LVE Y KAQG+WR PG EP ++D
Sbjct: 303 IANMAPEYGATCGFFPVDQVTLDYLRLSGRPEATVQLVEQYCKAQGMWRLPGQEPSFSDT 362
Query: 367 LELDMGEVEASLAGPKRPQDRVALKNMKSSFELLMETAEGPAENREANLESEGGQ-TAVG 425
L LDM +VEASLAGPKRPQDRVAL + +F+ +E P LESEGG AVG
Sbjct: 363 LALDMDDVEASLAGPKRPQDRVALGQVSQAFDHFIELQPKPLAKEVGRLESEGGGGVAVG 422
Query: 426 VDDS-----YKHHASQPLEMNGEKSRLDPGAVVIAAITSCTNTSNPSVMMAAGLIAQKAV 480
D Y H G+ L GAVVIAAITSCTNTSNPSVMMAAGL+A+KA+
Sbjct: 423 NADQTGAVDYSHQ--------GQTHTLRDGAVVIAAITSCTNTSNPSVMMAAGLVAKKAL 474
Query: 481 QKGLSTKPWVKTSLAPGSKVVTDYLKVGGFQDDLDKLGFNLVGYGCTTCIGNSGPLPDAV 540
+KGL KPWVK+SLAPGSKVVTDY K G LD+LGF+LVGYGCTTCIGNSGPL +A+
Sbjct: 475 EKGLQRKPWVKSSLAPGSKVVTDYFKAAGLTPYLDQLGFDLVGYGCTTCIGNSGPLDEAI 534
Query: 541 EKAISDGDLTVASVLSGNRNFEGRVHPLVKTNWLASPPLVVAYALAGNVRLDLSQDPLGN 600
EKAI DLTVASVLSGNRNFEGRVHPLVKTNWLASPPLVVAYALAG+VRLDL++DPLG+
Sbjct: 535 EKAIGSADLTVASVLSGNRNFEGRVHPLVKTNWLASPPLVVAYALAGSVRLDLTRDPLGS 594
Query: 601 DKDGNPVYLKDLWPSQQEIAEAVEKVKTDMFRKEYAEVFDGDATWKSIKVPESKVYEWSD 660
KDG PVYL+D+WPSQQEIAEAV KV T MF KEYAEVF GDA W++I+VP++ Y W
Sbjct: 595 GKDGQPVYLRDIWPSQQEIAEAVAKVDTAMFHKEYAEVFAGDAQWQAIEVPQAATYVWQA 654
Query: 661 KSTYIQHPPFFEGLKEEPDAIDDIKDANILALLGDSVTTDHISPAGSFKPDTPAGKYLQE 720
STYIQHPPFF+G+ P I +I A +LALLGDSVTTDHISPAG+ K D+PAG+YL+E
Sbjct: 655 DSTYIQHPPFFDGIGGPPPQIANIHGARVLALLGDSVTTDHISPAGNIKTDSPAGRYLRE 714
Query: 721 HGVEPKDFNSYGSRRGNHEVMMRGTFANVRIRNEMLDGVEGGYTKFVPTGEQMAIYDAAM 780
GVEP+DFNSYGSRRGNHEVMMRGTFAN+RIRNEML G EGG T VPTGE+++IYDAAM
Sbjct: 715 QGVEPRDFNSYGSRRGNHEVMMRGTFANIRIRNEMLAGEEGGNTLHVPTGEKLSIYDAAM 774
Query: 781 KYQEKGTPLVVIAGKEYGTGSSRDWAAKGTRLLGVKAVVAESYERIHRSNLIGMGVMPLQ 840
+YQ++GTPL+VIAG+EYGTGSSRDWAAKGT LLGVKAV+AES+ERIHRSNL+GMGV+PLQ
Sbjct: 775 RYQQEGTPLLVIAGQEYGTGSSRDWAAKGTNLLGVKAVLAESFERIHRSNLVGMGVLPLQ 834
Query: 841 FPEGTDRKSLKLTGEETISIEGLSG-EIKPGQTLKMTVKYKDGSTETCELKSRIDTANEA 899
F G +RK L LTG+E I + GL G I PG +L + + +DG E E+ RIDT NE
Sbjct: 835 FKAGHNRKQLGLTGKEQIDVLGLDGAHIHPGMSLPLRITREDGQQEQIEVLCRIDTLNEV 894
Query: 900 VYFKHGGILHYVVREML 916
YFK GGILHYV+R+M+
Sbjct: 895 EYFKAGGILHYVLRQMI 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: 2361
Number of extensions: 105
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 PP_2112 PP_2112 (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.30177.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 1436.3 0.0 0 1436.1 0.0 1.0 1 lcl|FitnessBrowser__Putida:PP_2112 PP_2112 aconitate hydratase 1
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Putida:PP_2112 PP_2112 aconitate hydratase 1
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1436.1 0.0 0 0 1 876 [] 18 911 .. 18 911 .. 0.97
Alignments for each domain:
== domain 1 score: 1436.1 bits; conditional E-value: 0
TIGR01341 1 kkvyyyslkaleeslekisklpkslrillesvlrnldgskikeedveallkwkkeelkdeeiafkparvvlqdft 75
k+++y+sl +++ +l+++++lp sl++lle++lr+ dg +++ +d+ a+++w e +d+ei+++parv++qdft
lcl|FitnessBrowser__Putida:PP_2112 18 KTYHYFSLTEAARQLGDLQRLPMSLKVLLENLLRWEDGATVTGDDLRAIAQWLGERRSDREIQYRPARVLMQDFT 92
689************************************************************************ PP
TIGR01341 76 Gvpavvdlaalreavknlgkdpekinplvpvdlvidhsvqvdkageeealeanvelefernkerykflkwakkaf 150
Gvpavvdlaa+r a+++ g+dp++inpl+pvdlvidhsv vd++g+ +a+++nv++e++rn ery+fl+w++ af
lcl|FitnessBrowser__Putida:PP_2112 93 GVPAVVDLAAMRAAMAKAGGDPQRINPLSPVDLVIDHSVMVDRYGTPQAFAENVDIEMQRNGERYAFLRWGQSAF 167
*************************************************************************** PP
TIGR01341 151 knlkvvppgtGivhqvnleylakvvfeaekdgellaypdslvGtdshttminGlGvlGwGvGGieaeaallGqpv 225
n++vvppgtGi+hqvnleyl++ v++ e dg+++a+pd+lvGtdshttminGlGvlGwGvGGieaeaa+lGqpv
lcl|FitnessBrowser__Putida:PP_2112 168 DNFRVVPPGTGICHQVNLEYLGRTVWTREADGRTYAFPDTLVGTDSHTTMINGLGVLGWGVGGIEAEAAMLGQPV 242
*************************************************************************** PP
TIGR01341 226 slsvpeviGvkltGklreGvtatdlvltvtellrkkgvvgkfveffGeglkelsladratianmapeyGataaff 300
s+ +peviG+kltGklreG+tatdlvltvt++lrkkgvvgkfvef+G+gl+el+ladratianmapeyGat++ff
lcl|FitnessBrowser__Putida:PP_2112 243 SMLIPEVIGFKLTGKLREGITATDLVLTVTQMLRKKGVVGKFVEFYGDGLAELPLADRATIANMAPEYGATCGFF 317
*************************************************************************** PP
TIGR01341 301 piddvtlqylrltgrdedkvelvekylkaqelfvddseepkytdvveldlsdveasvaGpkrpqdrvalkevkaa 375
p+d+vtl+ylrl+gr+e +v+lve+y+kaq++++ ++ep ++d++ ld++dveas+aGpkrpqdrval +v +a
lcl|FitnessBrowser__Putida:PP_2112 318 PVDQVTLDYLRLSGRPEATVQLVEQYCKAQGMWRLPGQEPSFSDTLALDMDDVEASLAGPKRPQDRVALGQVSQA 392
*************************************************************************** PP
TIGR01341 376 fkss..lesnagekglalr...............keakekklegkeaelkdgavviaaitsctntsnpsvllgag 433
f + l+ + k+++ a+++ +g++++l+dgavviaaitsctntsnpsv+++ag
lcl|FitnessBrowser__Putida:PP_2112 393 FDHFieLQPKPLAKEVGRLeseggggvavgnadqTGAVDYSHQGQTHTLRDGAVVIAAITSCTNTSNPSVMMAAG 467
*987333334444544432355666666665554445666667******************************** PP
TIGR01341 434 llakkavelGlkvkpyvktslapGskvvtdylaesgllpyleelGfnlvGyGcttciGnsGpleeeveeaikend 508
l+akka+e Gl++kp+vk+slapGskvvtdy++ +gl+pyl++lGf+lvGyGcttciGnsGpl+e++e+ai d
lcl|FitnessBrowser__Putida:PP_2112 468 LVAKKALEKGLQRKPWVKSSLAPGSKVVTDYFKAAGLTPYLDQLGFDLVGYGCTTCIGNSGPLDEAIEKAIGSAD 542
*************************************************************************** PP
TIGR01341 509 levsavlsGnrnfegrihplvkanylaspplvvayalaGtvdidlekepigtdkdGkkvylkdiwpsakeiaelv 583
l+v++vlsGnrnfegr+hplvk+n+laspplvvayalaG+v +dl+++p+g +kdG++vyl+diwps++eiae+v
lcl|FitnessBrowser__Putida:PP_2112 543 LTVASVLSGNRNFEGRVHPLVKTNWLASPPLVVAYALAGSVRLDLTRDPLGSGKDGQPVYLRDIWPSQQEIAEAV 617
*************************************************************************66 PP
TIGR01341 584 kkavkkelfkkeyeevtegnerwnelevtssdlyewdekstyireppffeelklepeevedikgarillllGdsi 658
+v + +f+key+ev+ g+++w+ +ev++ ++y w+ +styi++ppff+++ p ++ +i+gar+l+llGds+
lcl|FitnessBrowser__Putida:PP_2112 618 -AKVDTAMFHKEYAEVFAGDAQWQAIEVPQAATYVWQADSTYIQHPPFFDGIGGPPPQIANIHGARVLALLGDSV 691
.679*********************************************************************** PP
TIGR01341 659 ttdhispaGsikkdspaakylkekGverrdfnsyGsrrGnhevmlrGtfaniriknklvkgkeGgltvylpdsev 733
ttdhispaG+ik dspa++yl+e+Gve+rdfnsyGsrrGnhevm+rGtfaniri+n+++ g+eGg t+++p++e+
lcl|FitnessBrowser__Putida:PP_2112 692 TTDHISPAGNIKTDSPAGRYLREQGVEPRDFNSYGSRRGNHEVMMRGTFANIRIRNEMLAGEEGGNTLHVPTGEK 766
*************************************************************************** PP
TIGR01341 734 vsvydaamkykkegvplvvlaGkeyGsGssrdwaakgtkllGvkaviaesferihrsnlvgmGvlplefkqgeda 808
+s+ydaam+y++eg+pl+v+aG+eyG+Gssrdwaakgt+llGvkav+aesferihrsnlvgmGvlpl+fk+g+++
lcl|FitnessBrowser__Putida:PP_2112 767 LSIYDAAMRYQQEGTPLLVIAGQEYGTGSSRDWAAKGTNLLGVKAVLAESFERIHRSNLVGMGVLPLQFKAGHNR 841
*************************************************************************** PP
TIGR01341 809 etlgltgeetidvddie..elkpkkevtvelvkedgeketveavlridtevelayvkkgGilqyvlrkll 876
+ lgltg+e+idv +++ +++p+ ++++++++edg++e +e+ +ridt e++y+k gGil+yvlr+++
lcl|FitnessBrowser__Putida:PP_2112 842 KQLGLTGKEQIDVLGLDgaHIHPGMSLPLRITREDGQQEQIEVLCRIDTLNEVEYFKAGGILHYVLRQMI 911
*************9975338***********************************************986 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: 0.04u 0.02s 00:00:00.06 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.
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