Align Aconitate hydratase (EC 4.2.1.3) (characterized)
to candidate WP_090272412.1 BLU11_RS05430 aconitate hydratase AcnA
Query= reanno::Marino:GFF3491
(919 letters)
>NCBI__GCF_900105005.1:WP_090272412.1
Length = 911
Score = 1263 bits (3268), Expect = 0.0
Identities = 621/910 (68%), Positives = 735/910 (80%), Gaps = 5/910 (0%)
Query: 7 SKDSLNTLSSLDAGGKTFHYYSLPKAADTLGDLNRLPFSLKVLMENLLRNEDGTTVDRSH 66
S +SL TLSSL GG+T+ Y+SLPKA + LG++NRLP SLKVL+ENLLR+EDG TV R
Sbjct: 3 SINSLQTLSSLQVGGRTYQYHSLPKAGELLGEINRLPVSLKVLLENLLRHEDGDTVTRED 62
Query: 67 IDAMVQWMKDRHSDTEIQFRPARVLMQDFTGVPGVVDLAAMREAVQAAGKDPAMINPLSP 126
I AM WM +RHSD EIQ+RPARVLMQDFTGVP VVDLAAMR+AV AG DP INPLSP
Sbjct: 63 IQAMADWMINRHSDREIQYRPARVLMQDFTGVPAVVDLAAMRDAVARAGGDPQRINPLSP 122
Query: 127 VDLVIDHSVMVDKFGDASSFKDNVAIEMERNQERYEFLRWGQQAFDNFRVVPPGTGICHQ 186
VDLVIDHSVMVD FGDA++F+ NVA+E++RN ERY FLRWGQ+AF+NFRVVPPGTGICHQ
Sbjct: 123 VDLVIDHSVMVDHFGDAAAFQGNVAMEIQRNGERYAFLRWGQKAFNNFRVVPPGTGICHQ 182
Query: 187 VNLEYLGKTVWQKDQDGKTIAYPDTLVGTDSHTTMINGLGILGWGVGGIEAEAAMLGQPV 246
VNLEYL ++VW + DG++ AYPDTLVGTDSHTTM+NGLG+LGWGVGGIEAEAAMLGQPV
Sbjct: 183 VNLEYLAQSVWAAEVDGQSWAYPDTLVGTDSHTTMVNGLGVLGWGVGGIEAEAAMLGQPV 242
Query: 247 SMLIPEVVGFKITGKLREGITATDLVLTVTEMLRKKGVVGKFVEFYGDGLKDMPVADRAT 306
SMLIPEVVGFK+TGKLREG+TATDLVLTVT+MLRK GVVGKFVEFYGDGL D+P+ADRAT
Sbjct: 243 SMLIPEVVGFKLTGKLREGMTATDLVLTVTQMLRKHGVVGKFVEFYGDGLADLPLADRAT 302
Query: 307 IANMAPEYGATCGFFPVDEQTIKYMRLTGREEEQLELVEAYAKAQGLWREPGHEPVYTDN 366
IANMAPEYGATCGFFP+DE T+ Y+RLTGR E +E VEAY+KAQG+WREPGHEPV+TD
Sbjct: 303 IANMAPEYGATCGFFPIDEITLGYLRLTGRPAEVVERVEAYSKAQGMWREPGHEPVFTDT 362
Query: 367 LELDMGEVEASLAGPKRPQDRVALKNMKSSFELLMETAEGPAENREANLESEGGQTAVGV 426
L LDM EVE SLAGP+RPQDRV L ++ +F+ L+ + E + GG TAVG
Sbjct: 363 LHLDMNEVEPSLAGPRRPQDRVRLSDVPKAFDELLALQTSAVRDVERLEDEGGGGTAVGG 422
Query: 427 DDSYKHHASQPLEMNGEKSRLDPGAVVIAAITSCTNTSNPSVMMAAGLIAQKAVQKGLST 486
A + ++GE+ L GAVVIAAITSCTNTSNPSVMMAAGL+A+KA+++G+
Sbjct: 423 PS-----AEVCVTIDGEEHVLKNGAVVIAAITSCTNTSNPSVMMAAGLLARKAIERGIQR 477
Query: 487 KPWVKTSLAPGSKVVTDYLKVGGFQDDLDKLGFNLVGYGCTTCIGNSGPLPDAVEKAISD 546
KPWVK+SLAPGSKVVTDYL+ G LD+LGFNLVGYGCTTCIGNSGPLP+ + AIS+
Sbjct: 478 KPWVKSSLAPGSKVVTDYLERAGLTPYLDQLGFNLVGYGCTTCIGNSGPLPEPISHAISE 537
Query: 547 GDLTVASVLSGNRNFEGRVHPLVKTNWLASPPLVVAYALAGNVRLDLSQDPLGNDKDGNP 606
DL V++VLSGNRNFEGRVH VK NWLASPPLVVAYALAG+ RLDL ++PLG D+D P
Sbjct: 538 HDLVVSAVLSGNRNFEGRVHQQVKANWLASPPLVVAYALAGDSRLDLQEEPLGLDRDNKP 597
Query: 607 VYLKDLWPSQQEIAEAVEKVKTDMFRKEYAEVFDGDATWKSIKVPESKVYEWSDKSTYIQ 666
VYL+DLWPS EIAEAV V+ MFR YA+VF GD W+SI V Y W +STY+Q
Sbjct: 598 VYLRDLWPSNAEIAEAVALVEDSMFRSRYADVFTGDEHWQSIAVSGGDTYNWDGQSTYVQ 657
Query: 667 HPPFFEGLKEEPDAIDDIKDANILALLGDSVTTDHISPAGSFKPDTPAGKYLQEHGVEPK 726
+PP+FE + + + + I A +LA+ GDS+TTDHISPAG+ K +PAG+YLQ GV+P+
Sbjct: 658 NPPYFERIDQPIEPLQPIHQARVLAVFGDSITTDHISPAGNIKSSSPAGEYLQRLGVKPE 717
Query: 727 DFNSYGSRRGNHEVMMRGTFANVRIRNEMLDGVEGGYTKFVPTGEQMAIYDAAMKYQEKG 786
DFNSYGSRRGNHEVMMRGTFAN+RIRN ML G EGG T P+ E+M+IYDAAM+YQ++G
Sbjct: 718 DFNSYGSRRGNHEVMMRGTFANIRIRNRMLGGEEGGLTIHTPSSERMSIYDAAMRYQQEG 777
Query: 787 TPLVVIAGKEYGTGSSRDWAAKGTRLLGVKAVVAESYERIHRSNLIGMGVMPLQFPEGTD 846
TPLVV+AGKEYGTGSSRDWAAKGT LLGVKAV+AES+ERIHRSNL+GMGV+PLQF G +
Sbjct: 778 TPLVVLAGKEYGTGSSRDWAAKGTNLLGVKAVIAESFERIHRSNLVGMGVLPLQFVNGQN 837
Query: 847 RKSLKLTGEETISIEGLSGEIKPGQTLKMTVKYKDGSTETCELKSRIDTANEAVYFKHGG 906
+L+L G E + I G+ ++PGQ LK+ +G E+ RIDT+NE YFK GG
Sbjct: 838 APTLQLDGHEVLDIPGIDDNLRPGQILKIKATRSNGQQIEFEVVCRIDTSNEVDYFKAGG 897
Query: 907 ILHYVVREML 916
ILHYV+RE+L
Sbjct: 898 ILHYVLRELL 907
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: 2302
Number of extensions: 86
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: 911
Length adjustment: 43
Effective length of query: 876
Effective length of database: 868
Effective search space: 760368
Effective search space used: 760368
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 WP_090272412.1 BLU11_RS05430 (aconitate hydratase AcnA)
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.4113886.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 1419.4 0.0 0 1419.2 0.0 1.0 1 NCBI__GCF_900105005.1:WP_090272412.1
Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900105005.1:WP_090272412.1
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1419.2 0.0 0 0 2 876 .] 19 907 .. 18 907 .. 0.98
Alignments for each domain:
== domain 1 score: 1419.2 bits; conditional E-value: 0
TIGR01341 2 kvyyyslkaleeslekisklpkslrillesvlrnldgskikeedveallkwkkeelkdeeiafkparvvlqdf 74
+++y+sl+++ e l++i++lp sl++lle++lr+ dg +++ ed++a+++w ++ ++d+ei+++parv++qdf
NCBI__GCF_900105005.1:WP_090272412.1 19 TYQYHSLPKAGELLGEINRLPVSLKVLLENLLRHEDGDTVTREDIQAMADWMINRHSDREIQYRPARVLMQDF 91
789********************************************************************** PP
TIGR01341 75 tGvpavvdlaalreavknlgkdpekinplvpvdlvidhsvqvdkageeealeanvelefernkerykflkwak 147
tGvpavvdlaa+r+av++ g+dp++inpl+pvdlvidhsv vd++g+ a++ nv +e++rn ery+fl+w++
NCBI__GCF_900105005.1:WP_090272412.1 92 TGVPAVVDLAAMRDAVARAGGDPQRINPLSPVDLVIDHSVMVDHFGDAAAFQGNVAMEIQRNGERYAFLRWGQ 164
************************************************************************* PP
TIGR01341 148 kafknlkvvppgtGivhqvnleylakvvfeaekdgellaypdslvGtdshttminGlGvlGwGvGGieaeaal 220
kaf+n++vvppgtGi+hqvnleyla+ v++ae dg+ aypd+lvGtdshttm+nGlGvlGwGvGGieaeaa+
NCBI__GCF_900105005.1:WP_090272412.1 165 KAFNNFRVVPPGTGICHQVNLEYLAQSVWAAEVDGQSWAYPDTLVGTDSHTTMVNGLGVLGWGVGGIEAEAAM 237
************************************************************************* PP
TIGR01341 221 lGqpvslsvpeviGvkltGklreGvtatdlvltvtellrkkgvvgkfveffGeglkelsladratianmapey 293
lGqpvs+ +pev+G+kltGklreG+tatdlvltvt++lrk+gvvgkfvef+G+gl+ l+ladratianmapey
NCBI__GCF_900105005.1:WP_090272412.1 238 LGQPVSMLIPEVVGFKLTGKLREGMTATDLVLTVTQMLRKHGVVGKFVEFYGDGLADLPLADRATIANMAPEY 310
************************************************************************* PP
TIGR01341 294 GataaffpiddvtlqylrltgrdedkvelvekylkaqelfvddseepkytdvveldlsdveasvaGpkrpqdr 366
Gat++ffpid+ tl ylrltgr+ + ve ve+y kaq+++++ ++ep++td++ ld+++ve+s+aGp+rpqdr
NCBI__GCF_900105005.1:WP_090272412.1 311 GATCGFFPIDEITLGYLRLTGRPAEVVERVEAYSKAQGMWREPGHEPVFTDTLHLDMNEVEPSLAGPRRPQDR 383
************************************************************************* PP
TIGR01341 367 valkevkaafksslesna.gekglalr.............keakekklegkeaelkdgavviaaitsctntsn 425
v l++v++af + l ++ + +++ + +++g+e++lk+gavviaaitsctntsn
NCBI__GCF_900105005.1:WP_090272412.1 384 VRLSDVPKAFDELLALQTsAVRDVERLedeggggtavggpSAEVCVTIDGEEHVLKNGAVVIAAITSCTNTSN 456
***********99764431445543224778888888776667777889************************ PP
TIGR01341 426 psvllgagllakkavelGlkvkpyvktslapGskvvtdylaesgllpyleelGfnlvGyGcttciGnsGplee 498
psv+++aglla+ka+e G+++kp+vk+slapGskvvtdyl ++gl+pyl++lGfnlvGyGcttciGnsGpl+e
NCBI__GCF_900105005.1:WP_090272412.1 457 PSVMMAAGLLARKAIERGIQRKPWVKSSLAPGSKVVTDYLERAGLTPYLDQLGFNLVGYGCTTCIGNSGPLPE 529
************************************************************************* PP
TIGR01341 499 eveeaikendlevsavlsGnrnfegrihplvkanylaspplvvayalaGtvdidlekepigtdkdGkkvylkd 571
+++ai e dl+vsavlsGnrnfegr+h++vkan+laspplvvayalaG +dl++ep+g d+d k+vyl+d
NCBI__GCF_900105005.1:WP_090272412.1 530 PISHAISEHDLVVSAVLSGNRNFEGRVHQQVKANWLASPPLVVAYALAGDSRLDLQEEPLGLDRDNKPVYLRD 602
************************************************************************* PP
TIGR01341 572 iwpsakeiaelvkkavkkelfkkeyeevtegnerwnelevtssdlyewdekstyireppffeelklepeeved 644
+wps+ eiae+ v+ +f+ +y+ v+ g+e+w+++ v+ +d+y+wd +sty+++pp+fe + + e +++
NCBI__GCF_900105005.1:WP_090272412.1 603 LWPSNAEIAEA-VALVEDSMFRSRYADVFTGDEHWQSIAVSGGDTYNWDGQSTYVQNPPYFERIDQPIEPLQP 674
**********5.5789**************************************************999**** PP
TIGR01341 645 ikgarillllGdsittdhispaGsikkdspaakylkekGverrdfnsyGsrrGnhevmlrGtfaniriknklv 717
i++ar+l+++GdsittdhispaG+ik spa++yl+ Gv+++dfnsyGsrrGnhevm+rGtfaniri+n+++
NCBI__GCF_900105005.1:WP_090272412.1 675 IHQARVLAVFGDSITTDHISPAGNIKSSSPAGEYLQRLGVKPEDFNSYGSRRGNHEVMMRGTFANIRIRNRML 747
************************************************************************* PP
TIGR01341 718 kgkeGgltvylpdsevvsvydaamkykkegvplvvlaGkeyGsGssrdwaakgtkllGvkaviaesferihrs 790
g+eGglt++ p se +s+ydaam+y++eg+plvvlaGkeyG+Gssrdwaakgt+llGvkaviaesferihrs
NCBI__GCF_900105005.1:WP_090272412.1 748 GGEEGGLTIHTPSSERMSIYDAAMRYQQEGTPLVVLAGKEYGTGSSRDWAAKGTNLLGVKAVIAESFERIHRS 820
************************************************************************* PP
TIGR01341 791 nlvgmGvlplefkqgedaetlgltgeetidvddie.elkpkkevtvelvkedgeketveavlridtevelayv 862
nlvgmGvlpl+f +g++a tl+l+g+e +d+++i+ +l+p++ +++++++++g+++ +e+v+ridt+ e++y+
NCBI__GCF_900105005.1:WP_090272412.1 821 NLVGMGVLPLQFVNGQNAPTLQLDGHEVLDIPGIDdNLRPGQILKIKATRSNGQQIEFEVVCRIDTSNEVDYF 893
*********************************9637************************************ PP
TIGR01341 863 kkgGilqyvlrkll 876
k gGil+yvlr+ll
NCBI__GCF_900105005.1:WP_090272412.1 894 KAGGILHYVLRELL 907
***********986 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (876 nodes)
Target sequences: 1 (911 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 31.47
//
[ok]
This GapMind analysis is from Sep 24 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