Align aconitate hydratase (EC 4.2.1.3) (characterized)
to candidate WP_011386009.1 AMB_RS18485 aconitate hydratase AcnA
Query= BRENDA::A0A090AMG4
(901 letters)
>lcl|NCBI__GCF_000009985.1:WP_011386009.1 AMB_RS18485 aconitate
hydratase AcnA
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.32593.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: 0.07u 0.03s 00:00:00.10 Elapsed: 00:00:00.09
# Mc/sec: 8.61
//
[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 preprint 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