Align Aconitate hydratase B; ACN; Aconitase; (2R,3S)-2-methylisocitrate dehydratase; (2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate dehydratase; 2-methyl-cis-aconitate hydratase; Iron-responsive protein-like; IRP-like; RNA-binding protein; EC 4.2.1.3; EC 4.2.1.99 (characterized)
to candidate WP_057687520.1 ABB28_RS16835 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase
Query= SwissProt::Q8ZRS8
(865 letters)
>NCBI__GCF_001431535.1:WP_057687520.1
Length = 863
Score = 1261 bits (3264), Expect = 0.0
Identities = 625/859 (72%), Positives = 728/859 (84%), Gaps = 8/859 (0%)
Query: 1 MLEEYRKHVAERAAQGIVPKPLDATQMAALVELLKTPPVGEEEFLLDLLINRVPPGVDEA 60
MLE YR HVAERAA GI P PL A Q A ++ELLK PP GE EFLLDLL +RVP GVD+A
Sbjct: 1 MLEAYRHHVAERAALGIPPLPLTAQQTADVIELLKNPPAGEAEFLLDLLTHRVPAGVDDA 60
Query: 61 AYVKAGFLAAVAKGDTTSPLVSPEKAIELLGTMQGGYNIHPLIDALDDAKLAPIAAKALS 120
A VKA +LAA+A G +PL+S E+A ELLGTM GGYN+ PL+ LDDA + IAA AL
Sbjct: 61 AKVKASYLAAIAFGSEQNPLISRERATELLGTMLGGYNVAPLVQLLDDATVGSIAAAALK 120
Query: 121 HTLLMFDNFYDVEEKAKAGNEYAKQVMQSWADAEWFLSRPPLAEKITVTVFKVTGETNTD 180
+TLL+FD F+DV+EKAKAGN A+ V+QSWADAEWF SRP +A+ +T+TVFKV GETNTD
Sbjct: 121 NTLLVFDAFHDVQEKAKAGNANAQSVLQSWADAEWFTSRPEVAQSMTLTVFKVPGETNTD 180
Query: 181 DLSPAPDAWSRPDIPLHAQAMLKNARE--GIEPDQPGVVGPIKQIEALQKKGYPLAYVGD 238
DLSPAPDA +RPDIPLHA AMLKN R P++ G GPI++I +L+ KG+ +AYVGD
Sbjct: 181 DLSPAPDATTRPDIPLHALAMLKNKRPDAAFVPEEDGKRGPIQEILSLKDKGHLVAYVGD 240
Query: 239 VVGTGSSRKSATNSVLWFMGDDIPNVPNKRGGGLCLGGKIAPIFFNTMEDAGALPIEVDV 298
VVGTGSSRKSATNSVLWF G+DIP +PNKR GG+CLG KIAPIF+NTMEDAGALPIE+DV
Sbjct: 241 VVGTGSSRKSATNSVLWFTGEDIPFIPNKRFGGVCLGSKIAPIFYNTMEDAGALPIELDV 300
Query: 299 SNLNMGDVIDVYPYKGEVRNHETGELLATFELKTDVLIDEVRAGGRIPLIIGRGLTTKAR 358
+ + GDVI++ PY G+ + GE++A F++K+DVL DEVRAGGRIPLI+GRGLT KAR
Sbjct: 301 TQMEHGDVIELRPYDGKALKN--GEVIAEFQVKSDVLFDEVRAGGRIPLIVGRGLTAKAR 358
Query: 359 EALGLPHSDVFRQAKDVAESSRGFSLAQKMVGRACGV---KGIRPGAYCEPKMTSVGSQD 415
EALG+P +D+FR A++ +GFSLAQKMVGRACG+ +G+RPG YCEPKMTSVGSQD
Sbjct: 359 EALGMPVTDLFRLPVQPADTGKGFSLAQKMVGRACGLPEGQGMRPGTYCEPKMTSVGSQD 418
Query: 416 TTGPMTRDELKDLACLGFSADLVMQSFCHTAAYPKPVDVTTHHTLPDFIMNRGGVSLRPG 475
TTGPMTRDELKDLACLGFSADLVMQSFCHTAAYPKPVDV THHTLP+FI RGG+SLRPG
Sbjct: 419 TTGPMTRDELKDLACLGFSADLVMQSFCHTAAYPKPVDVKTHHTLPEFISTRGGISLRPG 478
Query: 476 DGVIHSWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVR 535
DGVIHSWLNRMLLPDTVGTGGDSHTRFP+GISFPAGSGLVAFAAATGVMPLDMPESVLVR
Sbjct: 479 DGVIHSWLNRMLLPDTVGTGGDSHTRFPVGISFPAGSGLVAFAAATGVMPLDMPESVLVR 538
Query: 536 FKGKMQPGITLRDLVHAIPLYAIKQGLLTVEKKGKKNIFSGRILEIEGLPDLKVEQAFEL 595
FKGKMQPG+TLRDLV+AIPLYAIK GLLTV K GKKNIFSGRILEIEGLPDLKVEQAFEL
Sbjct: 539 FKGKMQPGVTLRDLVNAIPLYAIKAGLLTVAKAGKKNIFSGRILEIEGLPDLKVEQAFEL 598
Query: 596 TDASAERSAAGCTIKLNKEPIVEYLTSNIVLLKWMIAEGYGDRRTLERRIQGMEKWLADP 655
+DASAERSAAGC++ L+K PI+EYLTSNI LL+WMIAEGY D R+L+RRI M++WLADP
Sbjct: 599 SDASAERSAAGCSVHLDKAPIIEYLTSNITLLQWMIAEGYQDPRSLQRRIDKMKEWLADP 658
Query: 656 QLLEADADAEYAAVIDIDLADIKEPILCAPNDPDDARLLSDVQGEKIDEVFIGSCMTNIG 715
QLL DADAEYAAVI+IDLADI EPI+ PNDPDD ++LS+V G KIDEVFIGSCMTNIG
Sbjct: 659 QLLAPDADAEYAAVIEIDLADIHEPIVACPNDPDDVKMLSEVAGAKIDEVFIGSCMTNIG 718
Query: 716 HFRAAGKLLDNHKGQLPTRLWVAPPTRMDAAQLTEEGYYSVFGKSGARIEIPGCSLCMGN 775
HFRAA KLL+ K +PT+LWVAPPT+MDA++LT EG+Y FG +GAR+E+PGCSLCMGN
Sbjct: 719 HFRAAAKLLEG-KRDIPTKLWVAPPTKMDASELTREGHYGTFGSAGARMEMPGCSLCMGN 777
Query: 776 QARVADGATVVSTSTRNFPNRLGTGANVFLASAELAAVAALIGKLPTPEEYQTYVAQVDK 835
QA+V +GATV STSTRNFPNRLG +NV+L SAELAA+ + +G++PT EEY V ++
Sbjct: 778 QAQVREGATVFSTSTRNFPNRLGRNSNVYLGSAELAAICSRLGRIPTKEEYMADVGVLEA 837
Query: 836 TAVDTYRYLNFDQLSQYTE 854
+ + YRY+NFDQ+ +Y E
Sbjct: 838 SGAEIYRYMNFDQIEEYQE 856
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: 2096
Number of extensions: 78
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 WP_057687520.1 ABB28_RS16835 (bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase)
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.11200.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 1503.8 0.0 0 1503.6 0.0 1.0 1 lcl|NCBI__GCF_001431535.1:WP_057687520.1 ABB28_RS16835 bifunctional aconi
Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_001431535.1:WP_057687520.1 ABB28_RS16835 bifunctional aconitate hydratase 2/2-methylisocitrate dehydra
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1503.6 0.0 0 0 1 844 [] 1 856 [. 1 856 [. 0.99
Alignments for each domain:
== domain 1 score: 1503.6 bits; conditional E-value: 0
TIGR00117 1 lleeyrkhvaeraaegiaplplnakqvaalvellkndpeaeeefllellidrvppgvdeaayvkagfla 69
+le+yr+hvaeraa+gi+plpl a+q+a+++ellkn+p++e+efll+ll++rvp gvd+aa+vka +la
lcl|NCBI__GCF_001431535.1:WP_057687520.1 1 MLEAYRHHVAERAALGIPPLPLTAQQTADVIELLKNPPAGEAEFLLDLLTHRVPAGVDDAAKVKASYLA 69
79******************************************************************* PP
TIGR00117 70 aiakgevksplisaeeavellgtmlggynvepliealeskdkniakaaakalsktllvfdafddveels 138
aia g + plis e+a+ellgtmlggynv pl+++l+ d+ + ++aa al++tllvfdaf+dv+e++
lcl|NCBI__GCF_001431535.1:WP_057687520.1 70 AIAFGSEQNPLISRERATELLGTMLGGYNVAPLVQLLD--DATVGSIAAAALKNTLLVFDAFHDVQEKA 136
**************************************..***************************** PP
TIGR00117 139 kt.neyakqvleswaeaewflnkeelaekitvtvfkvdgetntddlspapdaftrpdiplhalamlknk 206
k+ n+ a+ vl+swa+aewf ++e+a+ +t tvfkv+getntddlspapda+trpdiplhalamlknk
lcl|NCBI__GCF_001431535.1:WP_057687520.1 137 KAgNANAQSVLQSWADAEWFTSRPEVAQSMTLTVFKVPGETNTDDLSPAPDATTRPDIPLHALAMLKNK 205
**9****************************************************************** PP
TIGR00117 207 ieeieq............rikalkqkgvpvayvgdvvgtgssrksatnsvlwflgkdipfvpnkraggl 263
+++ +i +lk+kg+ vayvgdvvgtgssrksatnsvlwf g+dipf+pnkr gg+
lcl|NCBI__GCF_001431535.1:WP_057687520.1 206 RPDAAFvpeedgkrgpiqEILSLKDKGHLVAYVGDVVGTGSSRKSATNSVLWFTGEDIPFIPNKRFGGV 274
**988778999****99999************************************************* PP
TIGR00117 264 vlggkiapiffntaedsgalpievdvkdlnegdvikiypykgeitnketevvatfklkpetlldevrag 332
+lg kiapif+nt+ed+galpie dv ++++gdvi++ py+g+ k++ev+a f++k+++l+devrag
lcl|NCBI__GCF_001431535.1:WP_057687520.1 275 CLGSKIAPIFYNTMEDAGALPIELDVTQMEHGDVIELRPYDGKAL-KNGEVIAEFQVKSDVLFDEVRAG 342
*******************************************75.566******************** PP
TIGR00117 333 gripliigrgltdkarealglsesevfkkakapaesakgftlaqklvgkacgv...kgirpgtycepkv 398
gripli+grglt karealg++ +++f+ + +pa+++kgf+laqk+vg+acg+ +g+rpgtycepk+
lcl|NCBI__GCF_001431535.1:WP_057687520.1 343 GRIPLIVGRGLTAKAREALGMPVTDLFRLPVQPADTGKGFSLAQKMVGRACGLpegQGMRPGTYCEPKM 411
****************************************************87669************ PP
TIGR00117 399 ttvgsqdttgamtrdelkelaslgfdadlvlqsfchtaaypkpvdvkthktlpdfisqrggvalrpgdg 467
t+vgsqdttg+mtrdelk+la+lgf+adlv+qsfchtaaypkpvdvkth+tlp+fis+rgg++lrpgdg
lcl|NCBI__GCF_001431535.1:WP_057687520.1 412 TSVGSQDTTGPMTRDELKDLACLGFSADLVMQSFCHTAAYPKPVDVKTHHTLPEFISTRGGISLRPGDG 480
********************************************************************* PP
TIGR00117 468 vihswlnrmllpdtvgtggdshtrfplgisfpagsglvafaaatgvmpldmpesvlvrfkgelqpgitl 536
vihswlnrmllpdtvgtggdshtrfp+gisfpagsglvafaaatgvmpldmpesvlvrfkg++qpg+tl
lcl|NCBI__GCF_001431535.1:WP_057687520.1 481 VIHSWLNRMLLPDTVGTGGDSHTRFPVGISFPAGSGLVAFAAATGVMPLDMPESVLVRFKGKMQPGVTL 549
********************************************************************* PP
TIGR00117 537 rdlvnaipyyaikkglltvekkgkvnvfngrileieglpdlkveqafeltdasaersaagctiklnkep 605
rdlvnaip+yaik glltv k gk+n+f+grileieglpdlkveqafel+dasaersaagc ++l+k p
lcl|NCBI__GCF_001431535.1:WP_057687520.1 550 RDLVNAIPLYAIKAGLLTVAKAGKKNIFSGRILEIEGLPDLKVEQAFELSDASAERSAAGCSVHLDKAP 618
********************************************************************* PP
TIGR00117 606 vieylksnivllkemiaegyedkrtlkrridamekwlanpelleadadaeyaavieidlaeikepilaa 674
+ieyl sni ll++miaegy+d r+l+rrid+m++wla+p+ll +dadaeyaavieidla+i+epi+a+
lcl|NCBI__GCF_001431535.1:WP_057687520.1 619 IIEYLTSNITLLQWMIAEGYQDPRSLQRRIDKMKEWLADPQLLAPDADAEYAAVIEIDLADIHEPIVAC 687
********************************************************************* PP
TIGR00117 675 pndpddvkllsevagdaidevfigscmtnighfraagkileaaktvkarlwvvpptrmdeqqlieegyy 743
pndpddvk+lsevag +idevfigscmtnighfraa+k+le++++++++lwv+ppt+md+++l+ eg y
lcl|NCBI__GCF_001431535.1:WP_057687520.1 688 PNDPDDVKMLSEVAGAKIDEVFIGSCMTNIGHFRAAAKLLEGKRDIPTKLWVAPPTKMDASELTREGHY 756
********************************************************************* PP
TIGR00117 744 aifgaagartevpgcslcmgnqarvedgatvfststrnfdnrlgkgakvylgsaelaavaallgkiptk 812
+ fg+agar+e+pgcslcmgnqa+v++gatvfststrnf+nrlg+ ++vylgsaelaa+++ lg+iptk
lcl|NCBI__GCF_001431535.1:WP_057687520.1 757 GTFGSAGARMEMPGCSLCMGNQAQVREGATVFSTSTRNFPNRLGRNSNVYLGSAELAAICSRLGRIPTK 825
********************************************************************* PP
TIGR00117 813 eeylalvsekvesakdklyrylnfnelenfee 844
eey+a v + ++yry+nf+++e+++e
lcl|NCBI__GCF_001431535.1:WP_057687520.1 826 EEYMADVGVLEA-SGAEIYRYMNFDQIEEYQE 856
******986555.5566************985 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: 0.04u 0.02s 00:00:00.06 Elapsed: 00:00:00.06
# Mc/sec: 10.94
//
[ok]
This GapMind analysis is from Sep 24 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