Align aconitate hydratase (EC 4.2.1.3) (characterized)
to candidate N515DRAFT_1420 N515DRAFT_1420 aconitase
Query= BRENDA::P36683
(865 letters)
>FitnessBrowser__Dyella79:N515DRAFT_1420
Length = 863
Score = 1260 bits (3261), Expect = 0.0
Identities = 627/864 (72%), Positives = 734/864 (84%), Gaps = 8/864 (0%)
Query: 1 MLEEYRKHVAERAAEGIAPKPLDANQMAALVELLKNPPAGEEEFLLDLLTNRVPPGVDEA 60
ML YR+HVAERAA GI PL A Q A L+ELLKNPPAGEE FL+DL++NRVP GVD+A
Sbjct: 1 MLNAYRQHVAERAALGIPALPLTAQQTADLIELLKNPPAGEEAFLVDLISNRVPAGVDDA 60
Query: 61 AYVKAGFLAAIAKGEAKSPLLTPEKAIELLGTMQGGYNIHPLIDALDDAKLAPIAAKALS 120
A VKA +LAA+A G+ PLL+ KA ELLGTM GGYNIHPLI+ LDDA++ IAA AL
Sbjct: 61 AKVKASYLAAVAFGKEPCPLLSRAKATELLGTMLGGYNIHPLIELLDDAQVGGIAADALK 120
Query: 121 HTLLMFDNFYDVEEKAKAGNEYAKQVMQSWADAEWFLNRPALAEKLTVTVFKVTGETNTD 180
TLLMFD+F+DV+EKA GN AK V+QSWADAEWF +RP + LT+TVFKV GETNTD
Sbjct: 121 KTLLMFDSFHDVKEKADKGNANAKAVLQSWADAEWFTSRPEVPASLTITVFKVPGETNTD 180
Query: 181 DLSPAPDAWSRPDIPLHALAMLKNAREG--IEPDQPGVVGPIKQIEALQQKGFPLAYVGD 238
DLSPAPDA +RPDIPLHALAMLKN REG +P++ G GPI+QI+ L ++G +AYVGD
Sbjct: 181 DLSPAPDATTRPDIPLHALAMLKNKREGAPFQPEEDGKRGPIQQIQDLARQGHLVAYVGD 240
Query: 239 VVGTGSSRKSATNSVLWFMGDDIPHVPNKRGGGLCLGGKIAPIFFNTMEDAGALPIEVDV 298
VVGTGSSRKSATNSVLW+ G+DIP +PNKR GG+CLG KIAPIF+NTMEDAGALPIE+DV
Sbjct: 241 VVGTGSSRKSATNSVLWWTGEDIPFIPNKRFGGVCLGSKIAPIFYNTMEDAGALPIELDV 300
Query: 299 SNLNMGDVIDVYPYKGEVRNHETGELLATFELKTDVLIDEVRAGGRIPLIIGRGLTTKAR 358
S ++MGDV+++ PY+G+ + GE++A F++K+DVL DEVRAGGRIPLIIGRGLT KAR
Sbjct: 301 SQMDMGDVVELRPYEGKALKN--GEVIAEFQVKSDVLFDEVRAGGRIPLIIGRGLTAKAR 358
Query: 359 EALGLPHSDVFRQAKDVAESDRGFSLAQKMVGRACGV---KGIRPGAYCEPKMTSVGSQD 415
EALGL S +FR ++ A++ +G++LAQKMVGRACG+ +G+RPG YCEPKMTSVGSQD
Sbjct: 359 EALGLAPSTLFRLPQNPADTGKGYTLAQKMVGRACGLAEGEGVRPGTYCEPKMTSVGSQD 418
Query: 416 TTGPMTRDELKDLACLGFSADLVMQSFCHTAAYPKPVDVNTHHTLPDFIMNRGGVSLRPG 475
TTGPMTRDELKDLACLGFSADLVMQSFCHTAAYPKPVDV THH LP FI RGG+SLRPG
Sbjct: 419 TTGPMTRDELKDLACLGFSADLVMQSFCHTAAYPKPVDVKTHHELPAFISTRGGISLRPG 478
Query: 476 DGVIHSWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVR 535
DGVIHSWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVR
Sbjct: 479 DGVIHSWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVR 538
Query: 536 FKGKMQPGITLRDLVHAIPLYAIKQGLLTVEKKGKKNIFSGRILEIEGLPDLKVEQAFEL 595
FKG++QPG+TLRDLV+AIPLYAIKQGLLTV K+GK+NIFSGRILEIEGLP+LKVEQAFEL
Sbjct: 539 FKGELQPGVTLRDLVNAIPLYAIKQGLLTVAKQGKQNIFSGRILEIEGLPNLKVEQAFEL 598
Query: 596 TDASAERSAAGCTIKLNKEPIIEYLNSNIVLLKWMIAEGYGDRRTLERRIQGMEKWLANP 655
+DASAERSAAGCT++L++ PIIEYLNSNI LLK+MIA+GY D R+L RRI+ ME+WLANP
Sbjct: 599 SDASAERSAAGCTVRLDQAPIIEYLNSNITLLKYMIAQGYQDARSLSRRIKKMEEWLANP 658
Query: 656 ELLEADADAEYAAVIDIDLADIKEPILCAPNDPDDARPLSAVQGEKIDEVFIGSCMTNIG 715
+LLE DADAEYAAVI+IDLAD+ EPI+ PNDPDD + LS V G KIDEVFIGSCMTNIG
Sbjct: 659 QLLEPDADAEYAAVIEIDLADVHEPIVACPNDPDDVKSLSDVAGAKIDEVFIGSCMTNIG 718
Query: 716 HFRAAGKLLDAHKGQLPTRLWVAPPTRMDAAQLTEEGYYSVFGKSGARIEIPGCSLCMGN 775
HFRAA KLL+ K +PTRLWVAPPT+MD QLTEEG+Y V G +GAR+E+PGCSLCMGN
Sbjct: 719 HFRAASKLLEG-KRDIPTRLWVAPPTKMDQQQLTEEGHYGVLGTAGARMEMPGCSLCMGN 777
Query: 776 QARVADGATVVSTSTRNFPNRLGTGANVFLASAELAAVAALIGKLPTPEEYQTYVAQVDK 835
QA+V +GATV+STSTRNFPNRLG NV+L SAELAA+ + +G++PT EEY + ++
Sbjct: 778 QAQVREGATVMSTSTRNFPNRLGKNTNVYLGSAELAAICSRLGRIPTKEEYMADIGVINA 837
Query: 836 TAVDTYRYLNFNQLSQYTEKADGV 859
YRY+NF+Q++ + + AD V
Sbjct: 838 NGEKIYRYMNFDQIADFKQVADTV 861
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: 2066
Number of extensions: 79
Number of successful extensions: 5
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: 865
Length of database: 863
Length adjustment: 42
Effective length of query: 823
Effective length of database: 821
Effective search space: 675683
Effective search space used: 675683
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 N515DRAFT_1420 N515DRAFT_1420 (aconitase)
to HMM TIGR00117 (acnB: aconitate hydratase 2 (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/TIGR00117.hmm
# target sequence database: /tmp/gapView.14147.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: TIGR00117 [M=844]
Accession: TIGR00117
Description: acnB: aconitate hydratase 2
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 1510.9 0.0 0 1510.7 0.0 1.0 1 lcl|FitnessBrowser__Dyella79:N515DRAFT_1420 N515DRAFT_1420 aconitase
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dyella79:N515DRAFT_1420 N515DRAFT_1420 aconitase
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1510.7 0.0 0 0 1 843 [. 1 855 [. 1 856 [. 0.98
Alignments for each domain:
== domain 1 score: 1510.7 bits; conditional E-value: 0
TIGR00117 1 lleeyrkhvaeraaegiaplplnakqvaalvellkndpeaeeefllellidrvppgvdeaayvkag 66
+l++yr+hvaeraa+gi+ lpl a+q+a+l+ellkn+p++ee+fl++l+ +rvp gvd+aa+vka
lcl|FitnessBrowser__Dyella79:N515DRAFT_1420 1 MLNAYRQHVAERAALGIPALPLTAQQTADLIELLKNPPAGEEAFLVDLISNRVPAGVDDAAKVKAS 66
799*************************************************************** PP
TIGR00117 67 flaaiakgevksplisaeeavellgtmlggynvepliealeskdkniakaaakalsktllvfdafd 132
+laa+a g+ +pl+s +a+ellgtmlggyn++plie+l+ d+++ +aa al+ktll+fd+f+
lcl|FitnessBrowser__Dyella79:N515DRAFT_1420 67 YLAAVAFGKEPCPLLSRAKATELLGTMLGGYNIHPLIELLD--DAQVGGIAADALKKTLLMFDSFH 130
*****************************************..*********************** PP
TIGR00117 133 dveelskt.neyakqvleswaeaewflnkeelaekitvtvfkvdgetntddlspapdaftrpdipl 197
dv+e+++ n+ ak vl+swa+aewf ++e++ +t+tvfkv+getntddlspapda+trpdipl
lcl|FitnessBrowser__Dyella79:N515DRAFT_1420 131 DVKEKADKgNANAKAVLQSWADAEWFTSRPEVPASLTITVFKVPGETNTDDLSPAPDATTRPDIPL 196
*****9988********************************************************* PP
TIGR00117 198 halamlknkieeieq............rikalkqkgvpvayvgdvvgtgssrksatnsvlwflgkd 251
halamlknk+e+ +i++l ++g+ vayvgdvvgtgssrksatnsvlw+ g+d
lcl|FitnessBrowser__Dyella79:N515DRAFT_1420 197 HALAMLKNKREGAPFqpeedgkrgpiqQIQDLARQGHLVAYVGDVVGTGSSRKSATNSVLWWTGED 262
**********99755678999********************************************* PP
TIGR00117 252 ipfvpnkragglvlggkiapiffntaedsgalpievdvkdlnegdvikiypykgeitnketevvat 317
ipf+pnkr gg++lg kiapif+nt+ed+galpie dv+++++gdv+++ py+g+ k++ev+a
lcl|FitnessBrowser__Dyella79:N515DRAFT_1420 263 IPFIPNKRFGGVCLGSKIAPIFYNTMEDAGALPIELDVSQMDMGDVVELRPYEGKAL-KNGEVIAE 327
*******************************************************75.566***** PP
TIGR00117 318 fklkpetlldevraggripliigrgltdkarealglsesevfkkakapaesakgftlaqklvgkac 383
f++k+++l+devraggripliigrglt karealgl++s +f+ +++pa+++kg+tlaqk+vg+ac
lcl|FitnessBrowser__Dyella79:N515DRAFT_1420 328 FQVKSDVLFDEVRAGGRIPLIIGRGLTAKAREALGLAPSTLFRLPQNPADTGKGYTLAQKMVGRAC 393
****************************************************************** PP
TIGR00117 384 gv...kgirpgtycepkvttvgsqdttgamtrdelkelaslgfdadlvlqsfchtaaypkpvdvkt 446
g+ +g+rpgtycepk+t+vgsqdttg+mtrdelk+la+lgf+adlv+qsfchtaaypkpvdvkt
lcl|FitnessBrowser__Dyella79:N515DRAFT_1420 394 GLaegEGVRPGTYCEPKMTSVGSQDTTGPMTRDELKDLACLGFSADLVMQSFCHTAAYPKPVDVKT 459
*855569*********************************************************** PP
TIGR00117 447 hktlpdfisqrggvalrpgdgvihswlnrmllpdtvgtggdshtrfplgisfpagsglvafaaatg 512
h++lp fis+rgg++lrpgdgvihswlnrmllpdtvgtggdshtrfp+gisfpagsglvafaaatg
lcl|FitnessBrowser__Dyella79:N515DRAFT_1420 460 HHELPAFISTRGGISLRPGDGVIHSWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATG 525
****************************************************************** PP
TIGR00117 513 vmpldmpesvlvrfkgelqpgitlrdlvnaipyyaikkglltvekkgkvnvfngrileieglpdlk 578
vmpldmpesvlvrfkgelqpg+tlrdlvnaip+yaik+glltv k+gk n+f+grileieglp+lk
lcl|FitnessBrowser__Dyella79:N515DRAFT_1420 526 VMPLDMPESVLVRFKGELQPGVTLRDLVNAIPLYAIKQGLLTVAKQGKQNIFSGRILEIEGLPNLK 591
****************************************************************** PP
TIGR00117 579 veqafeltdasaersaagctiklnkepvieylksnivllkemiaegyedkrtlkrridamekwlan 644
veqafel+dasaersaagct++l++ p+ieyl+sni llk mia+gy+d+r+l rri++me+wlan
lcl|FitnessBrowser__Dyella79:N515DRAFT_1420 592 VEQAFELSDASAERSAAGCTVRLDQAPIIEYLNSNITLLKYMIAQGYQDARSLSRRIKKMEEWLAN 657
****************************************************************** PP
TIGR00117 645 pelleadadaeyaavieidlaeikepilaapndpddvkllsevagdaidevfigscmtnighfraa 710
p+lle+dadaeyaavieidla+++epi+a+pndpddvk+ls+vag +idevfigscmtnighfraa
lcl|FitnessBrowser__Dyella79:N515DRAFT_1420 658 PQLLEPDADAEYAAVIEIDLADVHEPIVACPNDPDDVKSLSDVAGAKIDEVFIGSCMTNIGHFRAA 723
****************************************************************** PP
TIGR00117 711 gkileaaktvkarlwvvpptrmdeqqlieegyyaifgaagartevpgcslcmgnqarvedgatvfs 776
+k+le+++++++rlwv+ppt+md+qql+eeg y+++g+agar+e+pgcslcmgnqa+v++gatv+s
lcl|FitnessBrowser__Dyella79:N515DRAFT_1420 724 SKLLEGKRDIPTRLWVAPPTKMDQQQLTEEGHYGVLGTAGARMEMPGCSLCMGNQAQVREGATVMS 789
****************************************************************** PP
TIGR00117 777 tstrnfdnrlgkgakvylgsaelaavaallgkiptkeeylalvsekvesakdklyrylnfnelenf 842
tstrnf+nrlgk ++vylgsaelaa+++ lg+iptkeey+a + ++++ +k+yry+nf+++ +f
lcl|FitnessBrowser__Dyella79:N515DRAFT_1420 790 TSTRNFPNRLGKNTNVYLGSAELAAICSRLGRIPTKEEYMADIGV-INANGEKIYRYMNFDQIADF 854
*****************************************9975.6667778***********99 PP
TIGR00117 843 e 843
+
lcl|FitnessBrowser__Dyella79:N515DRAFT_1420 855 K 855
7 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (844 nodes)
Target sequences: 1 (863 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: 0.06u 0.02s 00:00:00.08 Elapsed: 00:00:00.07
# Mc/sec: 9.68
//
[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