Align Aconitate hydratase (EC 4.2.1.3) (characterized)
to candidate N515DRAFT_1419 N515DRAFT_1419 aconitate hydratase
Query= reanno::Marino:GFF3491
(919 letters)
>FitnessBrowser__Dyella79:N515DRAFT_1419
Length = 916
Score = 1130 bits (2923), Expect = 0.0
Identities = 568/913 (62%), Positives = 694/913 (76%), Gaps = 11/913 (1%)
Query: 9 DSLNTLSSLDAGGKTFHYYSLPKAADTLGDLNRLPFSLKVLMENLLRNEDGTTVDRSHID 68
DS T +L G ++ SL K D+ LP+S+K+L+ENLLR+EDG V I+
Sbjct: 3 DSFATRDTLKVNGSSYQIASLAKLGQRF-DIKHLPYSMKILLENLLRHEDGVNVTAKEIE 61
Query: 69 AMVQWMKDRHSDTEIQFRPARVLMQDFTGVPGVVDLAAMREAVQAAGKDPAMINPLSPVD 128
A+ +W DTEI F PARV++QDFTGVP VVDLAAMR+AV G D INPL+P +
Sbjct: 62 AVARWNPKAEPDTEIAFMPARVVLQDFTGVPCVVDLAAMRDAVVKLGGDAKQINPLAPAE 121
Query: 129 LVIDHSVMVDKFGDASSFKDNVAIEMERNQERYEFLRWGQQAFDNFRVVPPGTGICHQVN 188
LVIDHSV VD +G S+ + NVAIE +RNQERY FLRWGQ+AFDNF+VVPP TGI HQVN
Sbjct: 122 LVIDHSVQVDVYGSESALEQNVAIEFQRNQERYAFLRWGQKAFDNFKVVPPRTGIVHQVN 181
Query: 189 LEYLGKTVWQKDQDGKTIAYPDTLVGTDSHTTMINGLGILGWGVGGIEAEAAMLGQPVSM 248
LEYLG+ V+ ++DG++ AYPDT+ GTDSHTTMING+G+LGWGVGGIEAEAAMLGQP SM
Sbjct: 182 LEYLGRVVFTGEKDGQSWAYPDTVFGTDSHTTMINGVGVLGWGVGGIEAEAAMLGQPSSM 241
Query: 249 LIPEVVGFKITGKLREGITATDLVLTVTEMLRKKGVVGKFVEFYGDGLKDMPVADRATIA 308
LIP+VVGFK+TGKL EG+TATDLVLTVT+MLRK GVVGKFVEF+G GLKD+ +ADRATI
Sbjct: 242 LIPQVVGFKLTGKLAEGVTATDLVLTVTQMLRKLGVVGKFVEFFGPGLKDLALADRATIG 301
Query: 309 NMAPEYGATCGFFPVDEQTIKYMRLTGREEEQLELVEAYAKAQGLWR-EPGHEPVYTDNL 367
NMAPEYGATCG FPVD++ + Y+RL+GR EE +ELV+AYA+AQGLW E +T L
Sbjct: 302 NMAPEYGATCGIFPVDQEALNYLRLSGRSEEHIELVKAYAQAQGLWHDENTPHAQFTTTL 361
Query: 368 ELDMGEVEASLAGPKRPQDRVALKNMKSSFELL---METAEGPAENREANLESEGGQTAV 424
ELD+G+V SLAGPKRPQDRV L++++ SF + P +N +EGG A+
Sbjct: 362 ELDLGDVRPSLAGPKRPQDRVLLQDVEKSFRDALGPLTANRRPRNGDTSNFINEGGSAAI 421
Query: 425 GVDDSYKHHASQPLEMNGEKSRLDPGAVVIAAITSCTNTSNPSVMMAAGLIAQKAVQKGL 484
G + + +E NGE RL GAVVIAAITSCTNTSNP+VM+ AGL+A+KA KGL
Sbjct: 422 GNPANAVSESGVLVEKNGESFRLGDGAVVIAAITSCTNTSNPAVMLGAGLLAKKAAAKGL 481
Query: 485 STKPWVKTSLAPGSKVVTDYLKVGGFQDDLDKLGFNLVGYGCTTCIGNSGPLPDAVEKAI 544
+PWVKTSL PGSKVVTDYL+ G +L+K+GF +VGYGCTTCIGNSGPLP + K I
Sbjct: 482 KAQPWVKTSLGPGSKVVTDYLEKTGLLQELEKVGFYVVGYGCTTCIGNSGPLPAEISKGI 541
Query: 545 SDGDLTVASVLSGNRNFEGRVHPLVKTNWLASPPLVVAYALAGNVRLDLSQDPLGNDKDG 604
++GDL VASVLSGNRNFEGRVHP VK N+LASPPLVVAYALAG++ +DLS+DPLG DG
Sbjct: 542 AEGDLAVASVLSGNRNFEGRVHPEVKMNYLASPPLVVAYALAGSLDVDLSKDPLGTGSDG 601
Query: 605 NPVYLKDLWPSQQEIAEAVE-KVKTDMFRKEYAEVFDGDATWKSIKVPESKVYEWSDKST 663
PVYL+D+WPS QEI++ + + MF K YA+VF GD W I P+ VY+W D ST
Sbjct: 602 QPVYLRDIWPSNQEISDTIAGAINPAMFAKNYADVFQGDDRWNHIASPDGSVYQWGD-ST 660
Query: 664 YIQHPPFFEGLKEEPDAIDDIKDANILALLGDSVTTDHISPAGSFKPDTPAGKYLQEHGV 723
YI++PP+F+G+ E ++DI A +L L GDS+TTDHISPAGS K D+PAG++L GV
Sbjct: 661 YIKNPPYFDGMTREVGKVEDIHGARVLGLFGDSITTDHISPAGSIKKDSPAGRFLIGKGV 720
Query: 724 EPKDFNSYGSRRGNHEVMMRGTFANVRIRNEMLDGVEGGYTKFVPTGEQMAIYDAAMKYQ 783
EPKDFNSYGSRRGN +VM+RGTFAN+RIRN MLDGVEGGYT VP+GEQ+AIYDAAMKY+
Sbjct: 721 EPKDFNSYGSRRGNDDVMVRGTFANIRIRNLMLDGVEGGYTLHVPSGEQLAIYDAAMKYK 780
Query: 784 EKGTPLVVIAGKEYGTGSSRDWAAKGTRLLGVKAVVAESYERIHRSNLIGMGVMPLQFPE 843
+ TPLVV+AGKEYGTGSSRDWAAKGT LLGVKAV+AES+ERIHRSNL+GMGV+P QF +
Sbjct: 781 AEHTPLVVLAGKEYGTGSSRDWAAKGTLLLGVKAVIAESFERIHRSNLVGMGVLPCQFED 840
Query: 844 GTDRKSLKLTGEETISIEGLS-GEIKPGQTLKMTVKYKDGSTETCELKSRIDTANEAVYF 902
G ++L LTG+E I GL+ GE K K+T DGS + +K + T E +F
Sbjct: 841 GQSAQTLGLTGKEVFDITGLNDGESK---VAKVTATAPDGSRKEFIVKVLLLTPKEREFF 897
Query: 903 KHGGILHYVVREM 915
+HGGIL YV+R++
Sbjct: 898 RHGGILQYVLRQL 910
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: 2290
Number of extensions: 103
Number of successful extensions: 6
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 N515DRAFT_1419 N515DRAFT_1419 (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.17507.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 1375.9 0.0 0 1375.3 0.0 1.2 1 lcl|FitnessBrowser__Dyella79:N515DRAFT_1419 N515DRAFT_1419 aconitate hydrata
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dyella79:N515DRAFT_1419 N515DRAFT_1419 aconitate hydratase
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1375.3 0.0 0 0 7 875 .. 22 910 .. 16 911 .. 0.96
Alignments for each domain:
== domain 1 score: 1375.3 bits; conditional E-value: 0
TIGR01341 7 slkaleeslekisklpkslrillesvlrnldgskikeedveallkwkkeelkdeeiafkparvvlq 72
sl +l + +i++lp+s++ille++lr+ dg +++ +++ea++ w+ ++ d+eiaf+parvvlq
lcl|FitnessBrowser__Dyella79:N515DRAFT_1419 22 SLAKLG-QRFDIKHLPYSMKILLENLLRHEDGVNVTAKEIEAVARWNPKAEPDTEIAFMPARVVLQ 86
555555.5678******************************************************* PP
TIGR01341 73 dftGvpavvdlaalreavknlgkdpekinplvpvdlvidhsvqvdkageeealeanvelefernke 138
dftGvp vvdlaa+r+av +lg+d+++inpl p++lvidhsvqvd++g+e+ale+nv +ef+rn+e
lcl|FitnessBrowser__Dyella79:N515DRAFT_1419 87 DFTGVPCVVDLAAMRDAVVKLGGDAKQINPLAPAELVIDHSVQVDVYGSESALEQNVAIEFQRNQE 152
****************************************************************** PP
TIGR01341 139 rykflkwakkafknlkvvppgtGivhqvnleylakvvfeaekdgellaypdslvGtdshttminGl 204
ry+fl+w++kaf n+kvvpp tGivhqvnleyl++vvf+ ekdg+ aypd++ GtdshttminG+
lcl|FitnessBrowser__Dyella79:N515DRAFT_1419 153 RYAFLRWGQKAFDNFKVVPPRTGIVHQVNLEYLGRVVFTGEKDGQSWAYPDTVFGTDSHTTMINGV 218
****************************************************************** PP
TIGR01341 205 GvlGwGvGGieaeaallGqpvslsvpeviGvkltGklreGvtatdlvltvtellrkkgvvgkfvef 270
GvlGwGvGGieaeaa+lGqp+s+ +p+v+G+kltGkl eGvtatdlvltvt++lrk gvvgkfvef
lcl|FitnessBrowser__Dyella79:N515DRAFT_1419 219 GVLGWGVGGIEAEAAMLGQPSSMLIPQVVGFKLTGKLAEGVTATDLVLTVTQMLRKLGVVGKFVEF 284
****************************************************************** PP
TIGR01341 271 fGeglkelsladratianmapeyGataaffpiddvtlqylrltgrdedkvelvekylkaqelfvd. 335
fG+glk l+ladrati nmapeyGat+++fp+d+++l+ylrl+gr+e+++elv++y++aq+l++d
lcl|FitnessBrowser__Dyella79:N515DRAFT_1419 285 FGPGLKDLALADRATIGNMAPEYGATCGIFPVDQEALNYLRLSGRSEEHIELVKAYAQAQGLWHDe 350
*****************************************************************5 PP
TIGR01341 336 dseepkytdvveldlsdveasvaGpkrpqdrvalkevkaafksslesnagekglalr......... 392
++ ++++t+++eldl dv++s+aGpkrpqdrv l++v+++f+ +l ++++
lcl|FitnessBrowser__Dyella79:N515DRAFT_1419 351 NTPHAQFTTTLELDLGDVRPSLAGPKRPQDRVLLQDVEKSFRDALGPLTANRRPRNGdtsnfineg 416
55669**************************************97654444432111223455678 PP
TIGR01341 393 .............keakekklegkeaelkdgavviaaitsctntsnpsvllgagllakkavelGlk 445
+ +g++ +l dgavviaaitsctntsnp+v+lgagllakka Glk
lcl|FitnessBrowser__Dyella79:N515DRAFT_1419 417 gsaaignpanavsESGVLVEKNGESFRLGDGAVVIAAITSCTNTSNPAVMLGAGLLAKKAAAKGLK 482
88888877764332222233359999**************************************** PP
TIGR01341 446 vkpyvktslapGskvvtdylaesgllpyleelGfnlvGyGcttciGnsGpleeeveeaikendlev 511
+p+vktsl pGskvvtdyl ++gll+ le++Gf++vGyGcttciGnsGpl+ e+++ i+e+dl v
lcl|FitnessBrowser__Dyella79:N515DRAFT_1419 483 AQPWVKTSLGPGSKVVTDYLEKTGLLQELEKVGFYVVGYGCTTCIGNSGPLPAEISKGIAEGDLAV 548
****************************************************************** PP
TIGR01341 512 savlsGnrnfegrihplvkanylaspplvvayalaGtvdidlekepigtdkdGkkvylkdiwpsak 577
++vlsGnrnfegr+hp vk nylaspplvvayalaG++d+dl+k+p+gt+ dG++vyl+diwps++
lcl|FitnessBrowser__Dyella79:N515DRAFT_1419 549 ASVLSGNRNFEGRVHPEVKMNYLASPPLVVAYALAGSLDVDLSKDPLGTGSDGQPVYLRDIWPSNQ 614
****************************************************************** PP
TIGR01341 578 eiaelvkkavkkelfkkeyeevtegnerwnelevtssdlyewdekstyireppffeelklepeeve 643
ei++++ a+++ +f k+y+ v++g++rwn++ +++++y+w +styi++pp+f++++ e +ve
lcl|FitnessBrowser__Dyella79:N515DRAFT_1419 615 EISDTIAGAINPAMFAKNYADVFQGDDRWNHIASPDGSVYQWG-DSTYIKNPPYFDGMTREVGKVE 679
******************************************6.7********************* PP
TIGR01341 644 dikgarillllGdsittdhispaGsikkdspaakylkekGverrdfnsyGsrrGnhevmlrGtfan 709
di+gar+l l+GdsittdhispaGsikkdspa+++l+ kGve++dfnsyGsrrGn++vm+rGtfan
lcl|FitnessBrowser__Dyella79:N515DRAFT_1419 680 DIHGARVLGLFGDSITTDHISPAGSIKKDSPAGRFLIGKGVEPKDFNSYGSRRGNDDVMVRGTFAN 745
****************************************************************** PP
TIGR01341 710 iriknklvkgkeGgltvylpdsevvsvydaamkykkegvplvvlaGkeyGsGssrdwaakgtkllG 775
iri+n +++g eGg+t+++p +e++++ydaamkyk e++plvvlaGkeyG+Gssrdwaakgt llG
lcl|FitnessBrowser__Dyella79:N515DRAFT_1419 746 IRIRNLMLDGVEGGYTLHVPSGEQLAIYDAAMKYKAEHTPLVVLAGKEYGTGSSRDWAAKGTLLLG 811
****************************************************************** PP
TIGR01341 776 vkaviaesferihrsnlvgmGvlplefkqgedaetlgltgeetidvddieelkpkkevtvelvked 841
vkaviaesferihrsnlvgmGvlp +f++g++a+tlgltg+e d+ ++++ + k ++v+++ d
lcl|FitnessBrowser__Dyella79:N515DRAFT_1419 812 VKAVIAESFERIHRSNLVGMGVLPCQFEDGQSAQTLGLTGKEVFDITGLNDGES-KVAKVTATAPD 876
***********************************************9999765.5689******* PP
TIGR01341 842 geketveavlridtevelayvkkgGilqyvlrkl 875
g+++ + +++ + t+ e +++++gGilqyvlr+l
lcl|FitnessBrowser__Dyella79:N515DRAFT_1419 877 GSRKEFIVKVLLLTPKEREFFRHGGILQYVLRQL 910
*******************************985 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: 0.04u 0.02s 00:00:00.06 Elapsed: 00:00:00.06
# Mc/sec: 12.05
//
[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