Align aconitate hydratase (EC 4.2.1.3) (characterized)
to candidate Dsui_2347 Dsui_2347 aconitate hydratase 1
Query= BRENDA::A0A090AMG4
(901 letters)
>FitnessBrowser__PS:Dsui_2347
Length = 898
Score = 1161 bits (3004), Expect = 0.0
Identities = 581/883 (65%), Positives = 701/883 (79%), Gaps = 9/883 (1%)
Query: 21 YYSLPALGKSLGID-VQRLPVSIRIVLESVLRNCDGKKVTEEHVKQLANWQANARREDEI 79
++SLPAL ++ GI V RLPVS+RIVLE++LR+CDG++VT HV QLANWQ A R +EI
Sbjct: 22 FHSLPAL-EAAGIGPVSRLPVSLRIVLEALLRHCDGRRVTPRHVLQLANWQPRAERTEEI 80
Query: 80 PFVVARVVLQDFTGVPLLADIAAMRSVADKMGKSPKSIEPLVPVDLVVDHSVMIDYFGTK 139
PFVVARVVLQDFTGVPLL D+AAMR A G PK IEPLVPVDLVVDHSV +D +GT
Sbjct: 81 PFVVARVVLQDFTGVPLLCDLAAMRDAAAAQGTDPKRIEPLVPVDLVVDHSVQVDEYGTP 140
Query: 140 NALDLNMKLEFKRNQERYQFMKWGMQAFDTFGVVPPGFGIVHQVNLEYLARGVHLDKKNN 199
AL NM+LEF+RN ERYQFMKWGMQAFDTF VVPPG GIVHQVNLEYL RGV ++
Sbjct: 141 TALRRNMELEFQRNAERYQFMKWGMQAFDTFKVVPPGIGIVHQVNLEYLFRGVR--RQGE 198
Query: 200 VYYPDSLVGTDSHTTMINGIGVVGWGVGGIEAEAGMLGQPVYFLTPDVVGVELKGQLRGG 259
+ +PD+LVGTDSHTTMING+GVVGWGVGGIEAEA MLGQPVYFLTPDVVGVEL+G+L G
Sbjct: 199 LLFPDTLVGTDSHTTMINGVGVVGWGVGGIEAEAAMLGQPVYFLTPDVVGVELRGRLNEG 258
Query: 260 VTATDLVLTITEMLRREKVVGKFVEFCGEGTASLSVAERATIGNMAPEYGATMGFFPVDE 319
VTATDLVLT+TE+LRREKVVGKFVEF G G+ SLS+ +RATI NMAPEYGAT+GFFPVDE
Sbjct: 259 VTATDLVLTVTELLRREKVVGKFVEFFGPGSTSLSLTDRATIANMAPEYGATLGFFPVDE 318
Query: 320 RTIDYFRGTGRTEAEIAAFEAYFKAQKMFGVPKAADINFTKLLTLDLSTVAPSLAGPKRP 379
+T+DY R TGR EAE+ AFEAYF+AQ +FG P+A DI+++ L+LDL+T+ PSLAGPKRP
Sbjct: 319 KTVDYLRQTGRNEAEVEAFEAYFRAQGLFGAPRAGDIDYSTQLSLDLATIVPSLAGPKRP 378
Query: 380 QDRIEIGNVKNTFIDLYSKPVAENGFNQPAEKLAQTFTTS-AGTQVKNGDILIAAITSCT 438
QDRI++ ++ +F L+S+P + NGF +PAE+L Q T+ AG + +GD+LIAAITSCT
Sbjct: 379 QDRIDLSDMGRSFDTLFSQPTSANGFGKPAEQLPQRQPTARAGVDLGHGDVLIAAITSCT 438
Query: 439 NTSNPSVLLAAGLLAKKAVEAGLTVPKHIKTSLAPGSRVVTEYLTKTGLLPYLEKLGFDV 498
NTSNP+VL+AAGLLAKKAV+ GL+V HIKTSLAPGSRVVT+YL K GLL L +LGF +
Sbjct: 439 NTSNPAVLIAAGLLAKKAVDKGLSVQPHIKTSLAPGSRVVTDYLEKAGLLAPLARLGFAL 498
Query: 499 AAYGCTTCIGNAGDLTPDLNEAIIGNDLICSAVLSGNRNFEARIHPNIKANFLASPPLVV 558
A YGCTTCIGNAGDL P+ N+AI DL+ +AVLSGNRNFEARIHP I+AN+LASPPLVV
Sbjct: 499 AGYGCTTCIGNAGDLAPEFNQAIAERDLVVAAVLSGNRNFEARIHPAIRANYLASPPLVV 558
Query: 559 AYALAGTVTRDLMTEPVGRGKNGD-VWLGDIWPTTEEIESLLKYALDPKAFEANYGQVKS 617
A+A+AG V DL T P+G G++G V+L +IWP++EEI ++L +A DP + Y +
Sbjct: 559 AFAIAGRVNVDLTTTPLGTGRDGQPVYLREIWPSSEEIATVLPFAQDPATYRRLYADF-T 617
Query: 618 NPGKLWENTKGVTGDTYNWPDSTYIAEPPFFEGFGMTPGAMPAVKGARALGVFGDSVTTD 677
LW G Y+WP STYIA PPFF+GF + P + + GARAL V GDSVTTD
Sbjct: 618 RDHDLWNAVPAPEGQIYDWPPSTYIARPPFFDGFTVEPPPLAPINGARALLVLGDSVTTD 677
Query: 678 HISPAGSIKETSPAGKWLKENGVMKADFNSYGSRRGNHEIMMRGTFANVRIKNLMIPALP 737
HISPAGS K +PAG+WL GV DFNSYGSRRG+HE+M+RGTFANVR+KNLM+P
Sbjct: 678 HISPAGSFKAATPAGQWLTAQGVKSLDFNSYGSRRGHHEVMVRGTFANVRVKNLMLPPKA 737
Query: 738 DGSRFEGGETLFQPTGEQMSIYDAAMKYVSAGTPTVVFGGEEYGTGSSRDWAAKGTQLLG 797
DGS EGG TL G+Q+++++AA Y G PT+VF GEEYGTGSSRDWAAKGT+LLG
Sbjct: 738 DGSPVEGGYTLLD--GQQVTVFEAASAYQQRGIPTLVFAGEEYGTGSSRDWAAKGTRLLG 795
Query: 798 VKAVITRSFERIHRSNLVGMGVLPLQFKGADSVQSLGITGEETYDISGLEDGIKPMQDVT 857
V+AV+ RSFERIHR+NLVGMGVLPLQFK S SLG+ G E +D+ G + ++ QD+
Sbjct: 796 VRAVVARSFERIHRANLVGMGVLPLQFKAGTSAASLGLDGSEHFDLPGADGPLQAQQDLM 855
Query: 858 LTITRKDGSKQDVTVLLRIDTPIEVDYYQHGGILPFVLRQLLA 900
L ITR DG + V +L RIDTPIEV+Y++HGGILP+VLRQLL+
Sbjct: 856 LRITRSDGRVEQVPLLCRIDTPIEVEYFRHGGILPYVLRQLLS 898
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: 2245
Number of extensions: 92
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: 898
Length adjustment: 43
Effective length of query: 858
Effective length of database: 855
Effective search space: 733590
Effective search space used: 733590
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 Dsui_2347 Dsui_2347 (aconitate hydratase 1)
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.31077.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 1237.5 0.0 0 1237.3 0.0 1.0 1 lcl|FitnessBrowser__PS:Dsui_2347 Dsui_2347 aconitate hydratase 1
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PS:Dsui_2347 Dsui_2347 aconitate hydratase 1
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1237.3 0.0 0 0 5 876 .] 22 897 .. 19 897 .. 0.97
Alignments for each domain:
== domain 1 score: 1237.3 bits; conditional E-value: 0
TIGR01341 5 yyslkalees.lekisklpkslrillesvlrnldgskikeedveallkwkkeelkdeeiafkparvvlqdftGvpav 80
++sl+ale + ++ +s+lp slri+le++lr++dg++++ ++v +l++w+ + + eei+f +arvvlqdftGvp++
lcl|FitnessBrowser__PS:Dsui_2347 22 FHSLPALEAAgIGPVSRLPVSLRIVLEALLRHCDGRRVTPRHVLQLANWQPRAERTEEIPFVVARVVLQDFTGVPLL 98
68999999876899*************************************************************** PP
TIGR01341 81 vdlaalreavknlgkdpekinplvpvdlvidhsvqvdkageeealeanvelefernkerykflkwakkafknlkvvp 157
dlaa+r+a ++ g dp++i+plvpvdlv+dhsvqvd++g+ +al+ n+elef+rn+ery+f+kw+ +af +kvvp
lcl|FitnessBrowser__PS:Dsui_2347 99 CDLAAMRDAAAAQGTDPKRIEPLVPVDLVVDHSVQVDEYGTPTALRRNMELEFQRNAERYQFMKWGMQAFDTFKVVP 175
***************************************************************************** PP
TIGR01341 158 pgtGivhqvnleylakvvfeaekdgellaypdslvGtdshttminGlGvlGwGvGGieaeaallGqpvslsvpeviG 234
pg Givhqvnleyl + v ++ +l++pd+lvGtdshttminG+Gv+GwGvGGieaeaa+lGqpv++ p+v+G
lcl|FitnessBrowser__PS:Dsui_2347 176 PGIGIVHQVNLEYLFRGVRRQG----ELLFPDTLVGTDSHTTMINGVGVVGWGVGGIEAEAAMLGQPVYFLTPDVVG 248
***************9997655....689************************************************ PP
TIGR01341 235 vkltGklreGvtatdlvltvtellrkkgvvgkfveffGeglkelsladratianmapeyGataaffpiddvtlqylr 311
v l G+l+eGvtatdlvltvtellr++ vvgkfveffG+g ++lsl+dratianmapeyGat +ffp+d++t++ylr
lcl|FitnessBrowser__PS:Dsui_2347 249 VELRGRLNEGVTATDLVLTVTELLRREKVVGKFVEFFGPGSTSLSLTDRATIANMAPEYGATLGFFPVDEKTVDYLR 325
***************************************************************************** PP
TIGR01341 312 ltgrdedkvelvekylkaqelfvd.dseepkytdvveldlsdveasvaGpkrpqdrvalkevkaafksslesnagek 387
tgr+e +ve e+y +aq+lf + ++ y++ + ldl ++ +s+aGpkrpqdr++l+++ ++f + ++++++ +
lcl|FitnessBrowser__PS:Dsui_2347 326 QTGRNEAEVEAFEAYFRAQGLFGApRAGDIDYSTQLSLDLATIVPSLAGPKRPQDRIDLSDMGRSFDTLFSQPTSAN 402
***********************98999************************************************* PP
TIGR01341 388 glalr..keakekklegkeaelkdgavviaaitsctntsnpsvllgagllakkavelGlkvkpyvktslapGskvvt 462
g++ + + ++++ l +g+v iaaitsctntsnp+vl++agllakkav+ Gl v+p++ktslapGs+vvt
lcl|FitnessBrowser__PS:Dsui_2347 403 GFGKPaeQLPQRQPTARAGVDLGHGDVLIAAITSCTNTSNPAVLIAAGLLAKKAVDKGLSVQPHIKTSLAPGSRVVT 479
**987446677777789999********************************************************* PP
TIGR01341 463 dylaesgllpyleelGfnlvGyGcttciGnsGpleeeveeaikendlevsavlsGnrnfegrihplvkanylasppl 539
dyl ++gll l +lGf l GyGcttciGn+G+l e ++ai+e dl+v+avlsGnrnfe+rihp ++anylasppl
lcl|FitnessBrowser__PS:Dsui_2347 480 DYLEKAGLLAPLARLGFALAGYGCTTCIGNAGDLAPEFNQAIAERDLVVAAVLSGNRNFEARIHPAIRANYLASPPL 556
***************************************************************************** PP
TIGR01341 540 vvayalaGtvdidlekepigtdkdGkkvylkdiwpsakeiaelvkkavkkelfkkeyeevtegnerwnelevtssdl 616
vva+a+aG+v++dl++ p+gt++dG++vyl++iwps +eia++ a + +++ y+ +t + + wn + ++++++
lcl|FitnessBrowser__PS:Dsui_2347 557 VVAFAIAGRVNVDLTTTPLGTGRDGQPVYLREIWPSSEEIATVLPFAQDPATYRRLYADFTRDHDLWNAVPAPEGQI 633
***************************************************************************** PP
TIGR01341 617 yewdekstyireppffeelklepeevedikgarillllGdsittdhispaGsikkdspaakylkekGverrdfnsyG 693
y+w styi +ppff+++++ep + +i+gar ll+lGds+ttdhispaGs k +pa+++l+ +Gv+ dfnsyG
lcl|FitnessBrowser__PS:Dsui_2347 634 YDWP-PSTYIARPPFFDGFTVEPPPLAPINGARALLVLGDSVTTDHISPAGSFKAATPAGQWLTAQGVKSLDFNSYG 709
***6.59********************************************************************** PP
TIGR01341 694 srrGnhevmlrGtfaniriknklvkgk......eGgltvylpdsevvsvydaamkykkegvplvvlaGkeyGsGssr 764
srrG hevm+rGtfan+r+kn +++ k eGg+t l d+++v+v++aa y++ g+p++v aG+eyG+Gssr
lcl|FitnessBrowser__PS:Dsui_2347 710 SRRGHHEVMVRGTFANVRVKNLMLPPKadgspvEGGYT--LLDGQQVTVFEAASAYQQRGIPTLVFAGEEYGTGSSR 784
***********************986522223367777..5699********************************* PP
TIGR01341 765 dwaakgtkllGvkaviaesferihrsnlvgmGvlplefkqgedaetlgltgeetidvdd.ieelkpkkevtvelvke 840
dwaakgt+llGv+av+a+sferihr+nlvgmGvlpl+fk+g++a +lgl+g+e+ d+++ l+ ++++ ++++++
lcl|FitnessBrowser__PS:Dsui_2347 785 DWAAKGTRLLGVRAVVARSFERIHRANLVGMGVLPLQFKAGTSAASLGLDGSEHFDLPGaDGPLQAQQDLMLRITRS 861
**********************************************************93457************** PP
TIGR01341 841 dgeketveavlridtevelayvkkgGilqyvlrkll 876
dg +e v +ridt++e++y+++gGil yvlr+ll
lcl|FitnessBrowser__PS:Dsui_2347 862 DGRVEQVPLLCRIDTPIEVEYFRHGGILPYVLRQLL 897
*********************************986 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (876 nodes)
Target sequences: 1 (898 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: 0.03u 0.02s 00:00:00.05 Elapsed: 00:00:00.06
# Mc/sec: 13.03
//
[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