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.27323.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: 13.19
//
[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