Align aconitate hydratase (EC 4.2.1.3) (characterized)
to candidate CA265_RS16405 CA265_RS16405 aconitate hydratase
Query= BRENDA::Q8RP87
(747 letters)
>FitnessBrowser__Pedo557:CA265_RS16405
Length = 759
Score = 985 bits (2547), Expect = 0.0
Identities = 485/747 (64%), Positives = 574/747 (76%), Gaps = 2/747 (0%)
Query: 1 MVYDLNMLKNFYASYKGKMEHVRAALKRPLTLAEKILYTHLYNVADLKNYERGEDYVNFR 60
M +D++M+K YA++ ++E R + RPLTL+EKILY HL++ ++RG DYV+F
Sbjct: 1 MAFDIDMIKKVYANFGSRVEAARKVVGRPLTLSEKILYAHLWDGDPKTAFKRGSDYVDFA 60
Query: 61 PDRVAMQDATAQMALLQFMNAGKEAVAVPSTVHCDHLIQAYRGAERDIETATQTNREVYD 120
PDRVAMQDATAQMALLQFM AG+ VAVPSTVHCDHLI A GA D+ A + EV+D
Sbjct: 61 PDRVAMQDATAQMALLQFMQAGRPQVAVPSTVHCDHLITAKEGAAIDLPHAKTESAEVFD 120
Query: 121 FLRDVSSRYGIGFWKPGAGIIHQVVLENYAFPGGMMVGTDSHTPNAGGLGMVAIGVGGAD 180
FL VS++YGIGFWKPGAGIIHQVVLENYAFPGGMM+GTDSHT NAGGLGMVAIGVGGAD
Sbjct: 121 FLSSVSNKYGIGFWKPGAGIIHQVVLENYAFPGGMMIGTDSHTVNAGGLGMVAIGVGGAD 180
Query: 181 AVDVMTGMEWELKMPKLIGVRLTGELNGWTAPKDVILKLAGILTVKGGTNAIIEYFGPGT 240
A DVM G+ WELK PKLIGV+LTG+LNGWTA KDVILK+AGILTVKGGT AI+EYFG G
Sbjct: 181 ACDVMAGLPWELKFPKLIGVKLTGKLNGWTAAKDVILKVAGILTVKGGTGAIVEYFGDGA 240
Query: 241 ASLSATGKATICNMGAEVGATTSLFPYDERMAVYLKATGREEVAAMADSVAADLRADDEV 300
S+S TGK TICNMGAE+GATTS F YDE M YL+ATGR EVA A+ +AA L D EV
Sbjct: 241 TSMSCTGKGTICNMGAEIGATTSTFGYDESMERYLRATGRNEVADEANKIAAYLTGDAEV 300
Query: 301 MARPDDFYDRVIEINLSELEPYINGPFTPDAATPISEFAEKVVTNGYPRKMEVGLIGSCT 360
A P++++D+VIEI+L LEPY+NGPFTPD ATP+S+ + NG+P K+E GLIGSCT
Sbjct: 301 YADPENYFDQVIEIDLDTLEPYLNGPFTPDLATPVSQMKVEAEKNGWPLKVEWGLIGSCT 360
Query: 361 NSSYQDISRAVSVARQVNEKNLGVAAPLIVNPGSEQIRATAERDGMMDVFEKMGATIMAN 420
NSSY+D+SRA S+A Q K L A +NPGSEQ+R TA+RDG + FE + ATI N
Sbjct: 361 NSSYEDLSRAASIANQAIAKGLVTKADFGINPGSEQVRYTADRDGFLKTFEDLNATIFTN 420
Query: 421 ACGPCIGQWKRHTDDPTRKNSIVTSFNRNFAKRADGNPNTFAFVASPEIVLALTIAGDLC 480
ACGPCIG W R + KN+IV SFNRNFAKRADGNPNTFAFVASPE+V A+ I+G+L
Sbjct: 421 ACGPCIGMWDRTGAEKAEKNTIVHSFNRNFAKRADGNPNTFAFVASPEMVAAIAISGNLG 480
Query: 481 FNPLKDRLVNHDGEKVKLSEPQGDELPSAGFVAGNQGYQAPG--GEKNEIRVAPDSQRLQ 538
FNPL D L N GE+VKL P G ELP+ GF + GYQAP G ++ V+P S RLQ
Sbjct: 481 FNPLTDTLTNDKGEQVKLDPPTGFELPTKGFAVEDAGYQAPAADGSSVQVLVSPTSHRLQ 540
Query: 539 LLTPFPAWDGNDFLNMPLLIKAQGKCTTDHISMAGPWLRFRGHLENISDNMLMGAVNAFN 598
LL PF W+G D + LLIKA+GKCTTDHISMAGPWL+FRGHL+NIS+NML+GAVN FN
Sbjct: 541 LLDPFTPWEGTDLQGLKLLIKAKGKCTTDHISMAGPWLKFRGHLDNISNNMLIGAVNYFN 600
Query: 599 GETNKVWNRLTNTYETVSGTAKQYKADGISSIVVAEENYGEGSSREHAAMEPRFLHVKVI 658
+T+ V N LT Y V T + YKA G+ SIVV +ENYGEGSSREHAAMEPR L V+ +
Sbjct: 601 DKTDNVKNELTGEYGPVPATQRDYKAAGLGSIVVGDENYGEGSSREHAAMEPRHLGVRAV 660
Query: 659 LAKSFARIHETNLKKQGMLAVTFADKADYDRIREHDLISVVGLKEFSPGRNLEVILHHED 718
L KSFARIHETNLKKQGML +TFADK DYD+I E D I ++GL EF+P + L ++LHH D
Sbjct: 661 LVKSFARIHETNLKKQGMLGLTFADKDDYDKILEDDTIDILGLTEFTPDQPLTLVLHHAD 720
Query: 719 GTEERFAVQHTYNEQQIGWFRAGSALN 745
GT+E F V H+YN QQI WF+AG ALN
Sbjct: 721 GTQESFPVNHSYNAQQIDWFKAGGALN 747
Lambda K H
0.317 0.134 0.395
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: 1540
Number of extensions: 53
Number of successful extensions: 2
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: 747
Length of database: 759
Length adjustment: 40
Effective length of query: 707
Effective length of database: 719
Effective search space: 508333
Effective search space used: 508333
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: 55 (25.8 bits)
Align candidate CA265_RS16405 CA265_RS16405 (aconitate hydratase)
to HMM TIGR01340 (aconitate hydratase, mitochondrial (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/TIGR01340.hmm
# target sequence database: /tmp/gapView.24751.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: TIGR01340 [M=745]
Accession: TIGR01340
Description: aconitase_mito: aconitate hydratase, mitochondrial
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 1106.2 0.0 0 1106.0 0.0 1.0 1 lcl|FitnessBrowser__Pedo557:CA265_RS16405 CA265_RS16405 aconitate hydratas
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Pedo557:CA265_RS16405 CA265_RS16405 aconitate hydratase
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1106.0 0.0 0 0 1 745 [] 12 749 .. 12 749 .. 0.98
Alignments for each domain:
== domain 1 score: 1106.0 bits; conditional E-value: 0
TIGR01340 1 yekllekldkvrrvlnsrpltlaekvlyshlddpeesllsqdiedvrGksylklkpdrvamqdasaqm 68
y+++ ++++ r+v++ rpltl+ek+ly+hl d + rG+ y+ + pdrvamqda+aqm
lcl|FitnessBrowser__Pedo557:CA265_RS16405 12 YANFGSRVEAARKVVG-RPLTLSEKILYAHLWDGDP---KTAF--KRGSDYVDFAPDRVAMQDATAQM 73
667778999999*999.****************998...3444..5********************** PP
TIGR01340 69 allqflsaglkkvavpasvhcdhlivakkGeekdlarakelnkevfdflesaakkygidfwkpGsGii 136
allqf+ ag ++vavp++vhcdhli ak+G+ dl++ak evfdfl s+++kygi+fwkpG+Gii
lcl|FitnessBrowser__Pedo557:CA265_RS16405 74 ALLQFMQAGRPQVAVPSTVHCDHLITAKEGAAIDLPHAKTESAEVFDFLSSVSNKYGIGFWKPGAGII 141
******************************************************************** PP
TIGR01340 137 hqivlenyavpGllmlGtdshtpnaGGlaaiaiGvGGadavdvlagipwelkapkvlGvkltGklsgw 204
hq+vlenya+pG++m+Gtdsht naGGl+++aiGvGGada dv+ag+pwelk pk++GvkltGkl+gw
lcl|FitnessBrowser__Pedo557:CA265_RS16405 142 HQVVLENYAFPGGMMIGTDSHTVNAGGLGMVAIGVGGADACDVMAGLPWELKFPKLIGVKLTGKLNGW 209
******************************************************************** PP
TIGR01340 205 tspkdvilklaglltvkGGtGaiveyfGeGveslsctGmaticnmGaeiGattslfpfneaskdylka 272
t++kdvilk+ag+ltvkGGtGaiveyfG+G s+sctG +ticnmGaeiGatts+f ++e++++yl+a
lcl|FitnessBrowser__Pedo557:CA265_RS16405 210 TAAKDVILKVAGILTVKGGTGAIVEYFGDGATSMSCTGKGTICNMGAEIGATTSTFGYDESMERYLRA 277
******************************************************************** PP
TIGR01340 273 tnraeiaeeak.vakd..kaellkadkdaeydelieidlsklephvnGpftpdlstpiskfkekvkke 337
t+r+e+a+ea+ +a + + ad + +d++ieidl++lep++nGpftpdl+tp+s++k +++k+
lcl|FitnessBrowser__Pedo557:CA265_RS16405 278 TGRNEVADEANkIAAYltGDAEVYADPENYFDQVIEIDLDTLEPYLNGPFTPDLATPVSQMKVEAEKN 345
*******999854444112344569******************************************* PP
TIGR01340 338 kwpeklkvGliGsctnssyedmsrvasivkdaekaGlkskidftvtpGseqiratlerdgilevfeka 405
+wp k++ GliGsctnssyed+sr+asi+++a +Gl +k+df + pGseq+r t +rdg l++fe+
lcl|FitnessBrowser__Pedo557:CA265_RS16405 346 GWPLKVEWGLIGSCTNSSYEDLSRAASIANQAIAKGLVTKADFGINPGSEQVRYTADRDGFLKTFEDL 413
******************************************************************** PP
TIGR01340 406 GgvvlanacGpciGqwdrkdvvkkgekntiltsynrnfrgrndanratmaflaspelvtalsvaGslk 473
+++++nacGpciG wdr +k eknti+ s+nrnf r d+n++t af+aspe+v+a++++G+l
lcl|FitnessBrowser__Pedo557:CA265_RS16405 414 NATIFTNACGPCIGMWDRTG-AEKAEKNTIVHSFNRNFAKRADGNPNTFAFVASPEMVAAIAISGNLG 480
*******************9.99********************************************* PP
TIGR01340 474 fnpltdslktkdGkefklkapkGdelpekgfeaGrdtfqaesdspdenvevavdpksdrlqllepfek 541
fnpltd+l++ +G + kl++p+G elp+kgf +qa++ + ++v+v v+p+s+rlqll+pf +
lcl|FitnessBrowser__Pedo557:CA265_RS16405 481 FNPLTDTLTNDKGEQVKLDPPTGFELPTKGFAVEDAGYQAPAAD-GSSVQVLVSPTSHRLQLLDPFTP 547
******************************************99.9********************** PP
TIGR01340 542 wngkdlkglrvlikvkGkcttdhisaaGpwlkykGhldnisentligavnaetgevnkvkdk.dGskg 608
w+g dl+gl++lik kGkcttdhis+aGpwlk++Ghldnis+n+ligavn+ +++ ++vk++ +G++g
lcl|FitnessBrowser__Pedo557:CA265_RS16405 548 WEGTDLQGLKLLIKAKGKCTTDHISMAGPWLKFRGHLDNISNNMLIGAVNYFNDKTDNVKNElTGEYG 615
************************************************************999***** PP
TIGR01340 609 avpelakdykargvkwvvvaeenyGeGsarehaaleprylGgriiivksfarihetnlkkqGvlpltf 676
vp++ +dyka g +vv++enyGeGs+rehaa+epr+lG r+++vksfarihetnlkkqG+l ltf
lcl|FitnessBrowser__Pedo557:CA265_RS16405 616 PVPATQRDYKAAGLGSIVVGDENYGEGSSREHAAMEPRHLGVRAVLVKSFARIHETNLKKQGMLGLTF 683
******************************************************************** PP
TIGR01340 677 aneadydkiqaedkvellnlkellknnngkevdlrvkkkngkvveiklkhtlskdqieffkaGsalnl 744
a++ dydki +d++++l+l+e+++ +++++l +++ +g ++ ++h+ + +qi++fkaG aln
lcl|FitnessBrowser__Pedo557:CA265_RS16405 684 ADKDDYDKILEDDTIDILGLTEFTP---DQPLTLVLHHADGTQESFPVNHSYNAQQIDWFKAGGALNI 748
************************9...99*************************************7 PP
TIGR01340 745 l 745
+
lcl|FitnessBrowser__Pedo557:CA265_RS16405 749 I 749
5 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (745 nodes)
Target sequences: 1 (759 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: 00:00:00.04
# Mc/sec: 12.18
//
[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