Align Aconitate hydratase A; ACN; Aconitase; (2R,3S)-2-methylisocitrate dehydratase; (2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate dehydratase; Iron-responsive protein-like; IRP-like; Probable 2-methyl-cis-aconitate hydratase; RNA-binding protein; EC 4.2.1.3; EC 4.2.1.99 (characterized)
to candidate WP_057687523.1 ABB28_RS16850 aconitate hydratase AcnA
Query= SwissProt::O53166
(943 letters)
>NCBI__GCF_001431535.1:WP_057687523.1
Length = 917
Score = 1103 bits (2852), Expect = 0.0
Identities = 558/944 (59%), Positives = 694/944 (73%), Gaps = 43/944 (4%)
Query: 7 NSFGAHDTLKVGEKSYQIYRLDAVP---NTAKLPYSLKVLAENLLRNEDGS-NITKDHIE 62
+SF L VG K Y + L + + + LPYS+K+L ENLLR+EDG + KDHIE
Sbjct: 3 DSFSTRSQLDVGGKRYDYFSLPKLGQRFDISHLPYSMKILLENLLRHEDGGVTVGKDHIE 62
Query: 63 AIANWDPKAEPSIEIQYTPARVVMQDFTGVPCIVDLATMREAIADLGGNPDKVNPLAPAD 122
A+A WDPKAEP IEI + PARVV+QDFTGVPC+VDLA MR+A+ LGG+P+++NP P++
Sbjct: 63 AVATWDPKAEPEIEIAFMPARVVLQDFTGVPCVVDLAAMRDAVVKLGGSPEQINPQIPSE 122
Query: 123 LVIDHSVIADLFGRADAFERNVEIEYQRNGERYQFLRWGQGAFDDFKVVPPGTGIVHQVN 182
LVIDHSV D+FG+ +A + N +IE+QRN ERY FLRWGQ AFD+FKVVPP TGIVHQVN
Sbjct: 123 LVIDHSVQVDVFGKPEALDLNGKIEFQRNQERYGFLRWGQKAFDNFKVVPPNTGIVHQVN 182
Query: 183 IEYLASVVMT--RDG--VAYPDTCVGTDSHTTMVNGLGVLGWGVGGIEAEAAMLGQPVSM 238
+E LA VVM +DG VAYPDT GTDSHTTM+NG+GVLGWGVGGIEAEAAMLGQP SM
Sbjct: 183 LENLARVVMAVDKDGTQVAYPDTVFGTDSHTTMINGIGVLGWGVGGIEAEAAMLGQPSSM 242
Query: 239 LIPRVVGFRLTGEIQPGVTATDVVLTVTEMLRQHGVVGKFVEFYGEGVAEVPLANRATLG 298
LIP+VVGF+LTG++ G TATD+VLTVT+MLR+HGVVGKFVEF+GEG+ +PLA+RAT+G
Sbjct: 243 LIPQVVGFKLTGQMPEGATATDLVLTVTQMLRKHGVVGKFVEFFGEGLQHLPLADRATIG 302
Query: 299 NMSPEFGSTAAIFPIDEETIKYLRFTGRTPEQVALVEAYAKAQGMWHDPKH-EPEFSEYL 357
NM+PE+G+T IFPID E++ YLR +GR EQ+ALVEAYAKAQG+WHD ++S L
Sbjct: 303 NMAPEYGATCGIFPIDHESLNYLRLSGRPEEQIALVEAYAKAQGLWHDADTAHAQYSATL 362
Query: 358 ELNLSDVVPSIAGPKRPQDRIALAQAKSTFREQIYHYVGNGSPDSPHDPHSKLDEVVEET 417
EL++ V PS+AGPKRPQDR+ L ++ +RE + N +V T
Sbjct: 363 ELDMGTVKPSLAGPKRPQDRVLLEDVQANYREALVGLTTNRDKK----------DVDVST 412
Query: 418 FPASDPGQLTFANDDVATDETVHSAAAHADGRVSNPVRVKSDELGEFVLDHGAVVIAAIT 477
F ++ G N+ +A + A DG+ F L GAVVIAAIT
Sbjct: 413 F-VNEGGGTAVGNEQLAKGQ----ADVELDGKA-------------FRLKDGAVVIAAIT 454
Query: 478 SCTNTSNPEVMLGAALLARNAVEKGLTSKPWVKTTIAPGSQVVNDYYDRSGLWPYLEKLG 537
SCTNTSNP VM+GA LLARNA +GL +PWVKT++ PGS+VV DY ++G+ LEKLG
Sbjct: 455 SCTNTSNPAVMIGAGLLARNAAARGLNRQPWVKTSLGPGSRVVTDYLSKAGVLTELEKLG 514
Query: 538 FYLVGYGCTTCIGNSGPLPEEISKAVNDNDLSVTAVLSGNRNFEGRINPDVKMNYLASPP 597
FY+VGYGCTTCIGNSGPLP E+S + DL VT+VLSGNRNFEGR++P+VKMNYLASPP
Sbjct: 515 FYVVGYGCTTCIGNSGPLPAEVSAGIALGDLVVTSVLSGNRNFEGRVHPEVKMNYLASPP 574
Query: 598 LVIAYALAGTMDFDFQTQPLGQDKDGKNVFLRDIWPSQQDVSDTIAAAINQEMFTRNYAD 657
LV+AYA+AGT D D T+PLG DG+ V+LRDIWPS +++ D IAA + EMF +NYAD
Sbjct: 575 LVVAYAIAGTTDIDLTTEPLGTGSDGQPVYLRDIWPSNKEIGDVIAATLGPEMFKQNYAD 634
Query: 658 VFKGDDRWRNLPTPSGNTFEWDPNSTYVRKPPYFEGMTAKPEPVGNISGARVLALLGDSV 717
VFKGD RW + +P G+ +EWD STY++ PPYF+GMT + + ++ GARV+ L GDS+
Sbjct: 635 VFKGDSRWNTIASPDGDLYEWDDGSTYIKNPPYFDGMTMQVGSIDDVHGARVMGLFGDSI 694
Query: 718 TTDHISPAGAIKPGTPAARYLDEHGVDRKDYNSFGSRRGNHEVMIRGTFANIRLRNQLLD 777
TTDHISPAG IK +PA R+L E GV D+NS+GSRRGN +VM+RGTFANIR++N +
Sbjct: 695 TTDHISPAGNIKKESPAGRFLQERGVQPADFNSYGSRRGNDDVMVRGTFANIRIKNLMFG 754
Query: 778 DVSGGYTRDFTQPGG--PQAFIYDAAQNYAAQHIPLVVFGGKEYGSGSSRDWAAKGTLLL 835
GG T + GG + IYDAA Y A +PLVV GKEYG+GSSRDWAAKGTLLL
Sbjct: 755 GEEGGNTLYYPASGGEPEKLAIYDAAIKYKADGVPLVVLAGKEYGTGSSRDWAAKGTLLL 814
Query: 836 GVRAVIAESFERIHRSNLIGMGVIPLQFPEGKSASSLGLDGTEVFDITGIDVLNDGKTPK 895
GV+AVIAESFERIHRSNL+GMGV+PLQF G++A SLGLDG+EVFDITG L DG + K
Sbjct: 815 GVKAVIAESFERIHRSNLVGMGVLPLQFRNGENAQSLGLDGSEVFDITG---LKDGAS-K 870
Query: 896 TVCVQATKGDGATIEFDAVVRIDTPGEADYYRNGGILQYVLRNI 939
V A K DG + F+A V + TP E +Y+R+GG+LQYVLR +
Sbjct: 871 RATVAAKKADGTVVTFEASVMLLTPKEVEYFRHGGLLQYVLRQL 914
Lambda K H
0.316 0.136 0.403
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: 2508
Number of extensions: 133
Number of successful extensions: 8
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: 943
Length of database: 917
Length adjustment: 43
Effective length of query: 900
Effective length of database: 874
Effective search space: 786600
Effective search space used: 786600
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 (21.6 bits)
S2: 57 (26.6 bits)
Align candidate WP_057687523.1 ABB28_RS16850 (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.32231.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 1360.8 0.0 0 1360.6 0.0 1.0 1 lcl|NCBI__GCF_001431535.1:WP_057687523.1 ABB28_RS16850 aconitate hydratas
Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_001431535.1:WP_057687523.1 ABB28_RS16850 aconitate hydratase AcnA
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1360.6 0.0 0 0 1 875 [. 16 914 .. 16 915 .. 0.98
Alignments for each domain:
== domain 1 score: 1360.6 bits; conditional E-value: 0
TIGR01341 1 kkvyyyslkaleeslekisklpkslrillesvlrnldg.skikeedveallkwkkeelkdeeiafkpar 68
k++ y+sl++l + +is+lp+s++ille++lr+ dg ++ ++++ea++ w+ ++ ++eiaf+par
lcl|NCBI__GCF_001431535.1:WP_057687523.1 16 KRYDYFSLPKLG-QRFDISHLPYSMKILLENLLRHEDGgVTVGKDHIEAVATWDPKAEPEIEIAFMPAR 83
5789*******9.7899********************736899************************** PP
TIGR01341 69 vvlqdftGvpavvdlaalreavknlgkdpekinplvpvdlvidhsvqvdkageeealeanvelefernk 137
vvlqdftGvp vvdlaa+r+av +lg+ pe+inp++p +lvidhsvqvd++g+ eal+ n ++ef+rn+
lcl|NCBI__GCF_001431535.1:WP_057687523.1 84 VVLQDFTGVPCVVDLAAMRDAVVKLGGSPEQINPQIPSELVIDHSVQVDVFGKPEALDLNGKIEFQRNQ 152
********************************************************************* PP
TIGR01341 138 erykflkwakkafknlkvvppgtGivhqvnleylakvvfeaekdgellaypdslvGtdshttminGlGv 206
ery fl+w++kaf n+kvvpp tGivhqvnle la+vv++ +kdg ++aypd++ GtdshttminG+Gv
lcl|NCBI__GCF_001431535.1:WP_057687523.1 153 ERYGFLRWGQKAFDNFKVVPPNTGIVHQVNLENLARVVMAVDKDGTQVAYPDTVFGTDSHTTMINGIGV 221
********************************************************************* PP
TIGR01341 207 lGwGvGGieaeaallGqpvslsvpeviGvkltGklreGvtatdlvltvtellrkkgvvgkfveffGegl 275
lGwGvGGieaeaa+lGqp+s+ +p+v+G+kltG++ eG tatdlvltvt++lrk+gvvgkfveffGegl
lcl|NCBI__GCF_001431535.1:WP_057687523.1 222 LGWGVGGIEAEAAMLGQPSSMLIPQVVGFKLTGQMPEGATATDLVLTVTQMLRKHGVVGKFVEFFGEGL 290
********************************************************************* PP
TIGR01341 276 kelsladratianmapeyGataaffpiddvtlqylrltgrdedkvelvekylkaqelfvd.dseepkyt 343
++l+ladrati nmapeyGat+++fpid+++l+ylrl+gr+e+++ lve+y+kaq+l++d d+++++y+
lcl|NCBI__GCF_001431535.1:WP_057687523.1 291 QHLPLADRATIGNMAPEYGATCGIFPIDHESLNYLRLSGRPEEQIALVEAYAKAQGLWHDaDTAHAQYS 359
************************************************************99999**** PP
TIGR01341 344 dvveldlsdveasvaGpkrpqdrvalkevkaafkss...lesnagekglalr................. 392
++eld+ +v++s+aGpkrpqdrv l++v+a+++++ l +n +k++ ++
lcl|NCBI__GCF_001431535.1:WP_057687523.1 360 ATLELDMGTVKPSLAGPKRPQDRVLLEDVQANYREAlvgLTTNRDKKDVDVStfvnegggtavgneqla 428
**********************************9944455666677787779999********99888 PP
TIGR01341 393 keakekklegkeaelkdgavviaaitsctntsnpsvllgagllakkavelGlkvkpyvktslapGskvv 461
k + + l+gk +lkdgavviaaitsctntsnp+v++gaglla+ a Gl+++p+vktsl pGs+vv
lcl|NCBI__GCF_001431535.1:WP_057687523.1 429 KGQADVELDGKAFRLKDGAVVIAAITSCTNTSNPAVMIGAGLLARNAAARGLNRQPWVKTSLGPGSRVV 497
888889999************************************************************ PP
TIGR01341 462 tdylaesgllpyleelGfnlvGyGcttciGnsGpleeeveeaikendlevsavlsGnrnfegrihplvk 530
tdyl+++g+l+ le+lGf++vGyGcttciGnsGpl+ ev+ i+ +dl+v++vlsGnrnfegr+hp vk
lcl|NCBI__GCF_001431535.1:WP_057687523.1 498 TDYLSKAGVLTELEKLGFYVVGYGCTTCIGNSGPLPAEVSAGIALGDLVVTSVLSGNRNFEGRVHPEVK 566
********************************************************************* PP
TIGR01341 531 anylaspplvvayalaGtvdidlekepigtdkdGkkvylkdiwpsakeiaelvkkavkkelfkkeyeev 599
nylaspplvvaya+aGt didl++ep+gt+ dG++vyl+diwps+kei +++ ++ +e+fk++y+ v
lcl|NCBI__GCF_001431535.1:WP_057687523.1 567 MNYLASPPLVVAYAIAGTTDIDLTTEPLGTGSDGQPVYLRDIWPSNKEIGDVIAATLGPEMFKQNYADV 635
********************************************************************* PP
TIGR01341 600 tegnerwnelevtssdlyewdekstyireppffeelklepeevedikgarillllGdsittdhispaGs 668
++g++rwn++ +++dlyewd+ styi++pp+f++++++ +++d++gar++ l+GdsittdhispaG+
lcl|NCBI__GCF_001431535.1:WP_057687523.1 636 FKGDSRWNTIASPDGDLYEWDDGSTYIKNPPYFDGMTMQVGSIDDVHGARVMGLFGDSITTDHISPAGN 704
********************************************************************* PP
TIGR01341 669 ikkdspaakylkekGverrdfnsyGsrrGnhevmlrGtfaniriknklvkgkeGgltvylpds....ev 733
ikk+spa+++l+e+Gv++ dfnsyGsrrGn++vm+rGtfanirikn + g+eGg t+y+p s e+
lcl|NCBI__GCF_001431535.1:WP_057687523.1 705 IKKESPAGRFLQERGVQPADFNSYGSRRGNDDVMVRGTFANIRIKNLMFGGEEGGNTLYYPASggepEK 773
*************************************************************65444489 PP
TIGR01341 734 vsvydaamkykkegvplvvlaGkeyGsGssrdwaakgtkllGvkaviaesferihrsnlvgmGvlplef 802
+++ydaa+kyk +gvplvvlaGkeyG+Gssrdwaakgt llGvkaviaesferihrsnlvgmGvlpl+f
lcl|NCBI__GCF_001431535.1:WP_057687523.1 774 LAIYDAAIKYKADGVPLVVLAGKEYGTGSSRDWAAKGTLLLGVKAVIAESFERIHRSNLVGMGVLPLQF 842
********************************************************************* PP
TIGR01341 803 kqgedaetlgltgeetidvddieelkpkkevtvelvkedgeketveavlridtevelayvkkgGilqyv 871
++ge+a++lgl+g+e d+ ++++ k++tv + k+dg + t+ea + + t+ e++y+++gG+lqyv
lcl|NCBI__GCF_001431535.1:WP_057687523.1 843 RNGENAQSLGLDGSEVFDITGLKDGA-SKRATVAAKKADGTVVTFEASVMLLTPKEVEYFRHGGLLQYV 910
********************999965.56899************************************* PP
TIGR01341 872 lrkl 875
lr+l
lcl|NCBI__GCF_001431535.1:WP_057687523.1 911 LRQL 914
*985 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (876 nodes)
Target sequences: 1 (917 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: 0.05u 0.02s 00:00:00.07 Elapsed: 00:00:00.07
# Mc/sec: 10.47
//
[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