Align aconitate hydratase (EC 4.2.1.3) (characterized)
to candidate WP_011386009.1 AMB_RS18485 aconitate hydratase AcnA
Query= BRENDA::A0A090AMG4
(901 letters)
>NCBI__GCF_000009985.1:WP_011386009.1
Length = 903
Score = 1139 bits (2945), Expect = 0.0
Identities = 571/898 (63%), Positives = 691/898 (76%), Gaps = 9/898 (1%)
Query: 9 LKNFKIGNKSC-QYYSLPALGKSLGIDVQRLPVSIRIVLESVLRNCDGKKVTEEHVKQLA 67
L++ +G++ +YY+L AL V RLPVSIRIVLESVLRNCDGK++TEEHV+QLA
Sbjct: 9 LRDLSLGHERLSRYYALAALDAVTDGPVSRLPVSIRIVLESVLRNCDGKRITEEHVRQLA 68
Query: 68 NWQANARREDEIPFVVARVVLQDFTGVPLLADIAAMRSVADKMGKSPKSIEPLVPVDLVV 127
NW+ +A R EIPFVVAR+VLQDFTGVPLL D+AAMR VA GK+PK IEPLVPVDLVV
Sbjct: 69 NWRPDAPRTQEIPFVVARIVLQDFTGVPLLCDLAAMRGVAQAFGKNPKIIEPLVPVDLVV 128
Query: 128 DHSVMIDYFGTKNALDLNMKLEFKRNQERYQFMKWGMQAFDTFGVVPPGFGIVHQVNLEY 187
DHSV +D++G ++LDLNM+ EF+RN ERY+F+KWGMQAFDTF VVPPG GIVHQVNLE+
Sbjct: 129 DHSVQVDHYGEADSLDLNMRREFQRNAERYRFIKWGMQAFDTFRVVPPGIGIVHQVNLEF 188
Query: 188 LARGVHLDKKNNVYYPDSLVGTDSHTTMINGIGVVGWGVGGIEAEAGMLGQPVYFLTPDV 247
LARGV +K+ + YPD+LVGTDSHTTMIN +GV GWGVGGIEAEAGMLGQP+ FLTPDV
Sbjct: 189 LARGVL--EKDGITYPDTLVGTDSHTTMINALGVAGWGVGGIEAEAGMLGQPLVFLTPDV 246
Query: 248 VGVELKGQLRGGVTATDLVLTITEMLRREKVVGKFVEFCGEGTASLSVAERATIGNMAPE 307
VGV L G+L G TATDLVL +TE LRR KVVGKFVEF GEGT SL+V +RATI NMAPE
Sbjct: 247 VGVHLHGRLPEGATATDLVLFLTERLRRAKVVGKFVEFFGEGTRSLAVPDRATIANMAPE 306
Query: 308 YGATMGFFPVDERTIDYFRGTGRTEAEIAAFEAYFKAQKMFGVPKAADINFTKLLTLDLS 367
YGATMGFFPVD+ T+ Y TGRT++EI F AY+ AQ +FG+P DI++++++ DL
Sbjct: 307 YGATMGFFPVDKETVRYLEATGRTDSEIEVFRAYYSAQGLFGMPMPGDIDYSEVIEFDLG 366
Query: 368 TVAPSLAGPKRPQDRIEIGNVKNTFIDLYSKPVAENGFNQPAEKLAQTFT--TSAGTQVK 425
+V PS+AGPKRPQDR+ + +++ F L+S P ++G+ +PAE L + T+A +
Sbjct: 367 SVQPSIAGPKRPQDRLNLSDMRRAFTSLFSAPAKDDGYGRPAEALGRRHRVETTAAADIG 426
Query: 426 NGDILIAAITSCTNTSNPSVLLAAGLLAKKAVEAGLTVPKHIKTSLAPGSRVVTEYLTKT 485
+GD+LIAAITSCTNTSNP V+LAAGLLA+KAV GL V +KTSLAPGSRVVTEYL K
Sbjct: 427 HGDVLIAAITSCTNTSNPGVMLAAGLLARKAVALGLKVGPRVKTSLAPGSRVVTEYLAKA 486
Query: 486 GLLPYLEKLGFDVAAYGCTTCIGNAGDLTPDLNEAIIGNDLICSAVLSGNRNFEARIHPN 545
GLL LE LGF V AYGCTTCIGN+G L PDL +AI +DL+C+AVLSGNRNFEARIHP
Sbjct: 487 GLLGDLESLGFGVVAYGCTTCIGNSGPLMPDLEQAIAADDLVCAAVLSGNRNFEARIHPA 546
Query: 546 IKANFLASPPLVVAYALAGTVTRDLMTEPVGRGKNGD-VWLGDIWPTTEEIESLLKYALD 604
IKANFL SPPLVVA+A+AG + D+ EP+G GK+G V L DIWP+ E+ L A D
Sbjct: 547 IKANFLMSPPLVVAFAIAGRIAIDMTQEPLGTGKDGKPVMLKDIWPSGREVADALLVATD 606
Query: 605 PKAFEANYGQ-VKSNPGKLWENTKGVTGDTYNWPDSTYIAEPPFFEGFGMTPGAMPAVKG 663
P+ + Y V NP LW + TG Y W STYIAEPPFFE F P + + G
Sbjct: 607 PELYRRLYSDFVHGNP--LWNDIPTQTGPAYAWETSTYIAEPPFFERFSPQPAGVGDIIG 664
Query: 664 ARALGVFGDSVTTDHISPAGSIKETSPAGKWLKENGVMKADFNSYGSRRGNHEIMMRGTF 723
ARAL +FGDSVTTDHISPAGSI +SPAG++L +GV DFNSYG+RRGNHE+MMRGTF
Sbjct: 665 ARALAIFGDSVTTDHISPAGSIAVSSPAGQYLLAHGVAAGDFNSYGARRGNHEVMMRGTF 724
Query: 724 ANVRIKNLMIPALPDGSRFEGGETLFQPTGEQMSIYDAAMKYVSAGTPTVVFGGEEYGTG 783
ANVRI+NLM+PA DGSR EGG TL QP G +M I+DAA +Y AG P++VF G EYGTG
Sbjct: 725 ANVRIRNLMLPAKVDGSRVEGGLTLHQPEGSEMPIFDAASRYQEAGIPSIVFAGTEYGTG 784
Query: 784 SSRDWAAKGTQLLGVKAVITRSFERIHRSNLVGMGVLPLQFKGADSVQSLGITGEETYDI 843
SSRDWAAKG +LLGV+AV+ +SFERIHRSNLVGMGVLPLQF+ +S SLGI G+E + +
Sbjct: 785 SSRDWAAKGPKLLGVRAVVAQSFERIHRSNLVGMGVLPLQFRDGESAASLGIAGDEEFHV 844
Query: 844 SGLEDGIKPMQDVTLTITRKDGSKQDVTVLLRIDTPIEVDYYQHGGILPFVLRQLLAA 901
GL ++P Q+V L I + G + +++ LR+DT IE+DY HGGILP+VLR LLAA
Sbjct: 845 RGLSGVLRPRQEVVLEIVNRQGRSRAISLQLRVDTAIELDYLSHGGILPYVLRDLLAA 902
Lambda K H
0.317 0.136 0.400
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: 2151
Number of extensions: 86
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: 901
Length of database: 903
Length adjustment: 43
Effective length of query: 858
Effective length of database: 860
Effective search space: 737880
Effective search space used: 737880
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: 41 (21.7 bits)
S2: 56 (26.2 bits)
Align candidate WP_011386009.1 AMB_RS18485 (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.29970.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 1260.9 0.0 0 1260.7 0.0 1.0 1 lcl|NCBI__GCF_000009985.1:WP_011386009.1 AMB_RS18485 aconitate hydratase
Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000009985.1:WP_011386009.1 AMB_RS18485 aconitate hydratase AcnA
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1260.7 0.0 0 0 4 876 .] 21 900 .. 18 900 .. 0.97
Alignments for each domain:
== domain 1 score: 1260.7 bits; conditional E-value: 0
TIGR01341 4 yyyslkalees.lekisklpkslrillesvlrnldgskikeedveallkwkkeelkdeeiafkparvvl 71
yy+l al+ ++ +s+lp s+ri+lesvlrn+dg++i+ee+v +l++w+ ++ + +ei+f +ar+vl
lcl|NCBI__GCF_000009985.1:WP_011386009.1 21 RYYALAALDAVtDGPVSRLPVSIRIVLESVLRNCDGKRITEEHVRQLANWRPDAPRTQEIPFVVARIVL 89
7******99765899****************************************************** PP
TIGR01341 72 qdftGvpavvdlaalreavknlgkdpekinplvpvdlvidhsvqvdkageeealeanvelefernkery 140
qdftGvp++ dlaa+r +++gk+p+ i+plvpvdlv+dhsvqvd++ge ++l+ n+++ef+rn+ery
lcl|NCBI__GCF_000009985.1:WP_011386009.1 90 QDFTGVPLLCDLAAMRGVAQAFGKNPKIIEPLVPVDLVVDHSVQVDHYGEADSLDLNMRREFQRNAERY 158
********************************************************************* PP
TIGR01341 141 kflkwakkafknlkvvppgtGivhqvnleylakvvfeaekdgellaypdslvGtdshttminGlGvlGw 209
+f+kw+ +af ++vvppg Givhqvnle+la+ v e++ ++ypd+lvGtdshttmin lGv+Gw
lcl|NCBI__GCF_000009985.1:WP_011386009.1 159 RFIKWGMQAFDTFRVVPPGIGIVHQVNLEFLARGVLEKD----GITYPDTLVGTDSHTTMINALGVAGW 223
***********************************9877....79************************ PP
TIGR01341 210 GvGGieaeaallGqpvslsvpeviGvkltGklreGvtatdlvltvtellrkkgvvgkfveffGeglkel 278
GvGGieaea++lGqp+ + p+v+Gv+l G+l eG tatdlvl +te lr+ vvgkfveffGeg ++l
lcl|NCBI__GCF_000009985.1:WP_011386009.1 224 GVGGIEAEAGMLGQPLVFLTPDVVGVHLHGRLPEGATATDLVLFLTERLRRAKVVGKFVEFFGEGTRSL 292
********************************************************************* PP
TIGR01341 279 sladratianmapeyGataaffpiddvtlqylrltgrdedkvelvekylkaqelfvd.dseepkytdvv 346
+++dratianmapeyGat++ffp+d++t+ yl+ tgr + ++e+ ++y aq+lf ++ y++v+
lcl|NCBI__GCF_000009985.1:WP_011386009.1 293 AVPDRATIANMAPEYGATMGFFPVDKETVRYLEATGRTDSEIEVFRAYYSAQGLFGMpMPGDIDYSEVI 361
*******************************************************9978899******* PP
TIGR01341 347 eldlsdveasvaGpkrpqdrvalkevkaafksslesnagekglalrkeak..ekkle.gkeaelkdgav 412
e dl +v++s+aGpkrpqdr++l+++++af+s ++ +a + g++ + ea ++ +e a + +g+v
lcl|NCBI__GCF_000009985.1:WP_011386009.1 362 EFDLGSVQPSIAGPKRPQDRLNLSDMRRAFTSLFSAPAKDDGYGRPAEALgrRHRVEtTAAADIGHGDV 430
*******************************************998766511444553566789***** PP
TIGR01341 413 viaaitsctntsnpsvllgagllakkavelGlkvkpyvktslapGskvvtdylaesgllpyleelGfnl 481
iaaitsctntsnp v+l+aglla+kav lGlkv p vktslapGs+vvt+yla++gll le lGf +
lcl|NCBI__GCF_000009985.1:WP_011386009.1 431 LIAAITSCTNTSNPGVMLAAGLLARKAVALGLKVGPRVKTSLAPGSRVVTEYLAKAGLLGDLESLGFGV 499
********************************************************************* PP
TIGR01341 482 vGyGcttciGnsGpleeeveeaikendlevsavlsGnrnfegrihplvkanylaspplvvayalaGtvd 550
v yGcttciGnsGpl ++e+ai+ +dl+ +avlsGnrnfe+rihp +kan+l+spplvva+a+aG++
lcl|NCBI__GCF_000009985.1:WP_011386009.1 500 VAYGCTTCIGNSGPLMPDLEQAIAADDLVCAAVLSGNRNFEARIHPAIKANFLMSPPLVVAFAIAGRIA 568
********************************************************************* PP
TIGR01341 551 idlekepigtdkdGkkvylkdiwpsakeiaelvkkavkkelfkkeyeevtegnerwnelevtssdlyew 619
id+++ep+gt+kdGk+v lkdiwps +e+a++ a +el+++ y+ +++gn wn++ + +++ y+w
lcl|NCBI__GCF_000009985.1:WP_011386009.1 569 IDMTQEPLGTGKDGKPVMLKDIWPSGREVADALLVATDPELYRRLYSDFVHGNPLWNDIPTQTGPAYAW 637
********************************************************************* PP
TIGR01341 620 dekstyireppffeelklepeevedikgarillllGdsittdhispaGsikkdspaakylkekGverrd 688
+ styi eppffe ++ +p+ v di gar l+ +Gds+ttdhispaGsi+ spa++yl +Gv d
lcl|NCBI__GCF_000009985.1:WP_011386009.1 638 E-TSTYIAEPPFFERFSPQPAGVGDIIGARALAIFGDSVTTDHISPAGSIAVSSPAGQYLLAHGVAAGD 705
6.79***************************************************************** PP
TIGR01341 689 fnsyGsrrGnhevmlrGtfaniriknklvkgk......eGgltvylpdsevvsvydaamkykkegvplv 751
fnsyG+rrGnhevm+rGtfan+ri+n ++++k eGglt++ p++ ++ ++daa +y++ g+p +
lcl|NCBI__GCF_000009985.1:WP_011386009.1 706 FNSYGARRGNHEVMMRGTFANVRIRNLMLPAKvdgsrvEGGLTLHQPEGSEMPIFDAASRYQEAGIPSI 774
****************************87643333448****************************** PP
TIGR01341 752 vlaGkeyGsGssrdwaakgtkllGvkaviaesferihrsnlvgmGvlplefkqgedaetlgltgeetid 820
v aG eyG+Gssrdwaakg+kllGv+av+a+sferihrsnlvgmGvlpl+f++ge+a +lg+ g+e+ +
lcl|NCBI__GCF_000009985.1:WP_011386009.1 775 VFAGTEYGTGSSRDWAAKGPKLLGVRAVVAQSFERIHRSNLVGMGVLPLQFRDGESAASLGIAGDEEFH 843
********************************************************************* PP
TIGR01341 821 vddiee.lkpkkevtvelvkedgeketveavlridtevelayvkkgGilqyvlrkll 876
v +++ l+p++ev +e+v+++g ++++ +lr+dt++el+y+++gGil yvlr+ll
lcl|NCBI__GCF_000009985.1:WP_011386009.1 844 VRGLSGvLRPRQEVVLEIVNRQGRSRAISLQLRVDTAIELDYLSHGGILPYVLRDLL 900
***875279*********************************************986 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (876 nodes)
Target sequences: 1 (903 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: 13.00
//
[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