Align Aconitate hydratase A; 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_057508738.1 ABB28_RS11325 Fe/S-dependent 2-methylisocitrate dehydratase AcnD
Query= SwissProt::Q937N8
(869 letters)
>NCBI__GCF_001431535.1:WP_057508738.1
Length = 871
Score = 1427 bits (3695), Expect = 0.0
Identities = 712/869 (81%), Positives = 777/869 (89%), Gaps = 3/869 (0%)
Query: 1 MNSANRKPLPGTKLDYFDARAAVEAIQPGAYDKLPYTSRVLAENLVRRCDPATLTDSLLQ 60
MN + RK LPGT LDYFD RAAV+AIQPGAY LPYTSRVLAENLVRRCDPATL SL Q
Sbjct: 1 MNESYRKNLPGTALDYFDTRAAVDAIQPGAYATLPYTSRVLAENLVRRCDPATLQASLRQ 60
Query: 61 LVGRKRDLDFPWFPARVVCHDILGQTALVDLAGLRDAIADQGGDPAKVNPVVPVQLIVDH 120
L+ R++DLDFPWFPARVVCHDILGQTALVDLAGLRDAIAD GGDPA++NPVVP QLIVDH
Sbjct: 61 LIERRQDLDFPWFPARVVCHDILGQTALVDLAGLRDAIADAGGDPAQINPVVPTQLIVDH 120
Query: 121 SLAVECGGFDPDAFAKNRAIEDRRNEDRFHFIDWTKQAFKNVDVIPPGNGIMHQINLEKM 180
SLAVE GFD AF +NRA+EDRRNEDRFHFI+WT++AFKNVDVIPPGNGIMHQINLEKM
Sbjct: 121 SLAVEYPGFDKAAFERNRAVEDRRNEDRFHFINWTRKAFKNVDVIPPGNGIMHQINLEKM 180
Query: 181 SPVIHADNGVAYPDTCVGTDSHTPHVDALGVIAIGVGGLEAENVMLGRASWMRLPDIVGV 240
SPV+ +GVA+PDTCVGTDSHTPHVDALGVIAIGVGGLEAE+VMLGRASWMRLPDI+GV
Sbjct: 181 SPVVQVRDGVAFPDTCVGTDSHTPHVDALGVIAIGVGGLEAESVMLGRASWMRLPDIIGV 240
Query: 241 ELTGKRQPGITATDIVLALTEFLRKEKVVGAYLEFRGEGASSLTLGDRATISNMAPEYGA 300
ELTG+ QPGIT TDIVLALTEFLR KVVGA++EF G GAS+L++GDRATISNM PE+GA
Sbjct: 241 ELTGRPQPGITCTDIVLALTEFLRAAKVVGAWIEFFGAGASALSIGDRATISNMTPEFGA 300
Query: 301 TAAMFFIDEQTIDYLRLTGRTDEQLKLVETYARTAGLWADSLKNAEYERVLKFDLSSVVR 360
TAAMF ID+QT+DYLRLTGR + Q++LVETYA+ AGLWAD L +YERVL+FDLSSVVR
Sbjct: 301 TAAMFSIDQQTLDYLRLTGREEPQVQLVETYAKAAGLWADDLAQVQYERVLQFDLSSVVR 360
Query: 361 NMAGPSNPHKRLPTSALAERGIAVDLDKASA--QEAEGLMPDGAVIIAAITSCTNTSNPR 418
NMAGPSNPHKR+ TS LA RGIA + AS ++A GLMPDGAVIIAAITSCTNTSNPR
Sbjct: 361 NMAGPSNPHKRVATSELAARGIADEAKLASGKLEQAGGLMPDGAVIIAAITSCTNTSNPR 420
Query: 419 NVIAAALLARNANARGLARKPWVKSSLAPGSKAVELYLEEANLLPDLEKLGFGIVAFACT 478
NVI AALLARNAN GL RKPWVKSSLAPGSKAV+LYLEEA LL +LE+LGFGIV FACT
Sbjct: 421 NVIGAALLARNANRAGLTRKPWVKSSLAPGSKAVQLYLEEAGLLGELEQLGFGIVGFACT 480
Query: 479 TCNGMSGALDPKIQQEIIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAG 538
TCNGMSGALDP IQQEIIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASP LVVAYAIAG
Sbjct: 481 TCNGMSGALDPVIQQEIIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPALVVAYAIAG 540
Query: 539 TIRFDIEKDVLGTDQDGKPVYLKDIWPSDEEIDAIVAKSVKPEQFRKVYEPMFAITAASG 598
T+RFDIEKD LG D G + LKD+WPSDEEIDA+V SVKPEQFRKVY+PMF T G
Sbjct: 541 TVRFDIEKDALGVDAQGNSITLKDLWPSDEEIDAVVKASVKPEQFRKVYDPMFTFTVEHG 600
Query: 599 ESVSPLYDWRPQSTYIRRPPYWEGALAGERTLKALRPLAVLGDNITTDHLSPSNAIMLNS 658
+SPLY WRPQSTYIRRPPYWEGALAG RTL +RPLAVLGDNITTDHLSPSNAI+ +S
Sbjct: 601 APISPLYAWRPQSTYIRRPPYWEGALAGARTLSGMRPLAVLGDNITTDHLSPSNAILASS 660
Query: 659 AAGEYLARMGLPEEDFNSYATHRGDHLTAQRATFANPTLINEMAVVDGQVKKGSLARIEP 718
AAGEYLA+MGLPEEDFNSYATHRGDHLTAQRATFANP LINEMAVVDG VK+GSLAR+EP
Sbjct: 661 AAGEYLAQMGLPEEDFNSYATHRGDHLTAQRATFANPKLINEMAVVDGVVKQGSLARVEP 720
Query: 719 EGKVVRMWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEVIVAEGFERIHR 778
EG+V+RMWEAIETYM R+QPLIIIAGADYGQGSSRDWAAKGVRLAGVE I AEGFERIHR
Sbjct: 721 EGQVLRMWEAIETYMLRRQPLIIIAGADYGQGSSRDWAAKGVRLAGVEAIAAEGFERIHR 780
Query: 779 TNLIGMGVLPLEFKPGVNRLTLGLDGTETYDVIGERQPRATLTLVVNRKNGERVEVPVTC 838
TNLIGMGVLPLEFKPGV RLTLG+DGTET+DV G R PRA LTLV++R++G ++ VPVTC
Sbjct: 781 TNLIGMGVLPLEFKPGVTRLTLGIDGTETFDVTGARLPRAELTLVIHRRDGSQLMVPVTC 840
Query: 839 RLDSDEEVSIYEAGGVL-HFAQDFLESSR 866
RLD+ EEVSIYEAGGVL FAQDFLE+S+
Sbjct: 841 RLDTAEEVSIYEAGGVLQRFAQDFLEASQ 869
Lambda K H
0.318 0.135 0.398
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: 2163
Number of extensions: 76
Number of successful extensions: 3
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: 869
Length of database: 871
Length adjustment: 42
Effective length of query: 827
Effective length of database: 829
Effective search space: 685583
Effective search space used: 685583
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_057508738.1 ABB28_RS11325 (Fe/S-dependent 2-methylisocitrate dehydratase AcnD)
to HMM TIGR02333 (acnD: 2-methylisocitrate dehydratase, Fe/S-dependent (EC 4.2.1.99))
# 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/TIGR02333.hmm
# target sequence database: /tmp/gapView.23035.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: TIGR02333 [M=858]
Accession: TIGR02333
Description: 2met_isocit_dHY: 2-methylisocitrate dehydratase, Fe/S-dependent
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 1767.6 0.1 0 1767.4 0.1 1.0 1 lcl|NCBI__GCF_001431535.1:WP_057508738.1 ABB28_RS11325 Fe/S-dependent 2-m
Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_001431535.1:WP_057508738.1 ABB28_RS11325 Fe/S-dependent 2-methylisocitrate dehydratase AcnD
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1767.4 0.1 0 0 1 858 [] 2 866 .. 2 866 .. 0.99
Alignments for each domain:
== domain 1 score: 1767.4 bits; conditional E-value: 0
TIGR02333 1 ntkyrkalpgtdldyfdaraaveaikpgaydklpytsrvlaenlvrrvdpetleaslkqlierkreldf 69
n+ yrk+lpgt+ldyfd+raav+ai+pgay++lpytsrvlaenlvrr+dp+tl+asl+qlier+++ldf
lcl|NCBI__GCF_001431535.1:WP_057508738.1 2 NESYRKNLPGTALDYFDTRAAVDAIQPGAYATLPYTSRVLAENLVRRCDPATLQASLRQLIERRQDLDF 70
789****************************************************************** PP
TIGR02333 70 pwyparvvchdilgqtalvdlaglrdaiaekggdpaqvnpvvetqlivdhslaveyggfdpdafeknra 138
pw+parvvchdilgqtalvdlaglrdaia+ ggdpaq+npvv+tqlivdhslavey gfd+ afe+nra
lcl|NCBI__GCF_001431535.1:WP_057508738.1 71 PWFPARVVCHDILGQTALVDLAGLRDAIADAGGDPAQINPVVPTQLIVDHSLAVEYPGFDKAAFERNRA 139
********************************************************************* PP
TIGR02333 139 iedrrnedrfhfinwtkkafknvdvipagngimhqinlekmspvvqvkegvafpdtlvgtdshtphvda 207
+edrrnedrfhfinwt+kafknvdvip+gngimhqinlekmspvvqv++gvafpdt+vgtdshtphvda
lcl|NCBI__GCF_001431535.1:WP_057508738.1 140 VEDRRNEDRFHFINWTRKAFKNVDVIPPGNGIMHQINLEKMSPVVQVRDGVAFPDTCVGTDSHTPHVDA 208
********************************************************************* PP
TIGR02333 208 lgviaigvggleaetvmlgraslmrlpdivgveltgkrqpgitatdivlalteflrkekvvsayleffg 276
lgviaigvggleae+vmlgras+mrlpdi+gveltg+ qpgit+tdivlalteflr+ kvv+a++effg
lcl|NCBI__GCF_001431535.1:WP_057508738.1 209 LGVIAIGVGGLEAESVMLGRASWMRLPDIIGVELTGRPQPGITCTDIVLALTEFLRAAKVVGAWIEFFG 277
********************************************************************* PP
TIGR02333 277 egakaltlgdratisnmtpeygataamfaideqtidylkltgreeeqvklvetyakaaglwadslkkav 345
ga al++gdratisnmtpe+gataamf id+qt+dyl+ltgree qv+lvetyakaaglwad+l + +
lcl|NCBI__GCF_001431535.1:WP_057508738.1 278 AGASALSIGDRATISNMTPEFGATAAMFSIDQQTLDYLRLTGREEPQVQLVETYAKAAGLWADDLAQVQ 346
********************************************************************* PP
TIGR02333 346 yervlkfdlssvvrnlagpsnpharlatsdlaakgiakevee......eaeglmpdgaviiaaitsctn 408
yervl+fdlssvvrn+agpsnph+r+ats+laa+gia e++ +a glmpdgaviiaaitsctn
lcl|NCBI__GCF_001431535.1:WP_057508738.1 347 YERVLQFDLSSVVRNMAGPSNPHKRVATSELAARGIADEAKLasgkleQAGGLMPDGAVIIAAITSCTN 415
*************************************99875555666899****************** PP
TIGR02333 409 tsnprnvvaagllarnanklglkrkpwvksslapgskvvklyleeagllkeleklgfgivafacttcng 477
tsnprnv+ a+llarnan+ gl+rkpwvksslapgsk+v+lyleeagll ele+lgfgiv+facttcng
lcl|NCBI__GCF_001431535.1:WP_057508738.1 416 TSNPRNVIGAALLARNANRAGLTRKPWVKSSLAPGSKAVQLYLEEAGLLGELEQLGFGIVGFACTTCNG 484
********************************************************************* PP
TIGR02333 478 msgaldpviqqeiidrdlyatavlsgnrnfdgrihpyakqaflaspplvvayaiagtirfdiekdvlgv 546
msgaldpviqqeiidrdlyatavlsgnrnfdgrihpyakqaflasp lvvayaiagt+rfdiekd+lgv
lcl|NCBI__GCF_001431535.1:WP_057508738.1 485 MSGALDPVIQQEIIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPALVVAYAIAGTVRFDIEKDALGV 553
********************************************************************* PP
TIGR02333 547 dadgkeirlkdiwpsdeeidavvaaavkpeqfrkvyipmfdle.daqkkvsplydwrpmstyirrppyw 614
da+g+ i lkd+wpsdeeidavv+a+vkpeqfrkvy pmf +++ sply wrp+styirrppyw
lcl|NCBI__GCF_001431535.1:WP_057508738.1 554 DAQGNSITLKDLWPSDEEIDAVVKASVKPEQFRKVYDPMFTFTvEHGAPISPLYAWRPQSTYIRRPPYW 622
*****************************************99899999******************** PP
TIGR02333 615 egalagertlkgmrplavlgdnittdhlspsnailldsaageylakmglpeedfnsyathrgdhltaqr 683
egalag rtl gmrplavlgdnittdhlspsnail++saageyla+mglpeedfnsyathrgdhltaqr
lcl|NCBI__GCF_001431535.1:WP_057508738.1 623 EGALAGARTLSGMRPLAVLGDNITTDHLSPSNAILASSAAGEYLAQMGLPEEDFNSYATHRGDHLTAQR 691
********************************************************************* PP
TIGR02333 684 atfanpklfnemvkedgkvkqgslariepegkvtrmweaietymnrkqpliiiagadygqgssrdwaak 752
atfanpkl+nem+ +dg vkqgslar+epeg+v rmweaietym r+qpliiiagadygqgssrdwaak
lcl|NCBI__GCF_001431535.1:WP_057508738.1 692 ATFANPKLINEMAVVDGVVKQGSLARVEPEGQVLRMWEAIETYMLRRQPLIIIAGADYGQGSSRDWAAK 760
********************************************************************* PP
TIGR02333 753 gvrlagveaivaegferihrtnlvgmgvlplefkpgtnrktlaldgtevydvvgeitpradltlvvtrk 821
gvrlagveai aegferihrtnl+gmgvlplefkpg+ r tl++dgte++dv g++ pra+ltlv++r+
lcl|NCBI__GCF_001431535.1:WP_057508738.1 761 GVRLAGVEAIAAEGFERIHRTNLIGMGVLPLEFKPGVTRLTLGIDGTETFDVTGARLPRAELTLVIHRR 829
********************************************************************* PP
TIGR02333 822 ngeklevpvtcrldtaeevsvyeaggvlqrfaqdfle 858
+g +l vpvtcrldtaeevs+yeaggvlqrfaqdfle
lcl|NCBI__GCF_001431535.1:WP_057508738.1 830 DGSQLMVPVTCRLDTAEEVSIYEAGGVLQRFAQDFLE 866
***********************************97 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (858 nodes)
Target sequences: 1 (871 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: 00:00:00.08
# Mc/sec: 9.10
//
[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