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_086511660.1 BZY95_RS20065 Fe/S-dependent 2-methylisocitrate dehydratase AcnD
Query= SwissProt::Q937N8
(869 letters)
>NCBI__GCF_002151265.1:WP_086511660.1
Length = 869
Score = 1401 bits (3627), Expect = 0.0
Identities = 700/866 (80%), Positives = 764/866 (88%), Gaps = 3/866 (0%)
Query: 1 MNSANRKPLPGTKLDYFDARAAVEAIQPGAYDKLPYTSRVLAENLVRRCDPATLTDSLLQ 60
MN+ RKPLPGT+LDYFD R AVE IQPGAYD LPYTSRVLAE LVRRC+P LTD+L Q
Sbjct: 1 MNTQYRKPLPGTELDYFDVREAVEEIQPGAYDTLPYTSRVLAEQLVRRCEPELLTDALKQ 60
Query: 61 LVGRKRDLDFPWFPARVVCHDILGQTALVDLAGLRDAIADQGGDPAKVNPVVPVQLIVDH 120
L+ R+RDLDFPW+PARVVCHDILGQTALVDLAGLRDAIA++GGDP+KVNPVVP QLIVDH
Sbjct: 61 LIERRRDLDFPWYPARVVCHDILGQTALVDLAGLRDAIAEKGGDPSKVNPVVPTQLIVDH 120
Query: 121 SLAVECGGFDPDAFAKNRAIEDRRNEDRFHFIDWTKQAFKNVDVIPPGNGIMHQINLEKM 180
SLAVECGG DPDAFAKNRAIEDRRNEDRFHFIDWT+ AFKNVDVIP GNGIMHQINLEKM
Sbjct: 121 SLAVECGGDDPDAFAKNRAIEDRRNEDRFHFIDWTRTAFKNVDVIPAGNGIMHQINLEKM 180
Query: 181 SPVIHADNGVAYPDTCVGTDSHTPHVDALGVIAIGVGGLEAENVMLGRASWMRLPDIVGV 240
SPVI A +GVAYPDTCVGTDSHTPH+D LGVIAIGVGGLEAE VMLGR S MRLPDIVGV
Sbjct: 181 SPVIQARDGVAYPDTCVGTDSHTPHIDCLGVIAIGVGGLEAETVMLGRPSMMRLPDIVGV 240
Query: 241 ELTGKRQPGITATDIVLALTEFLRKEKVVGAYLEFRGEGASSLTLGDRATISNMAPEYGA 300
ELTGKRQ GITATDIVLA+TEFLR+E+VVGAYLEF GEGA SLT+GDRATISNM PEYGA
Sbjct: 241 ELTGKRQSGITATDIVLAITEFLRQERVVGAYLEFFGEGADSLTIGDRATISNMTPEYGA 300
Query: 301 TAAMFFIDEQTIDYLRLTGRTDEQLKLVETYARTAGLWADSLKNAEYERVLKFDLSSVVR 360
TAAMF+ID+QT+DYL +TGR EQ+ LVE YA+T GLWADSLKN +YERVL FDLS+V R
Sbjct: 301 TAAMFYIDQQTLDYLAITGREPEQVALVENYAKTVGLWADSLKNVQYERVLTFDLSTVER 360
Query: 361 NMAGPSNPHKRLPTSALAERGIAVDLDKASAQEAEGLMPDGAVIIAAITSCTNTSNPRNV 420
N+AGPSNPH+RLPTSALAERGIAV+L+ A A+E G MPDGAVIIAAITSCTNTSNPRNV
Sbjct: 361 NLAGPSNPHRRLPTSALAERGIAVNLELALAEEKAGRMPDGAVIIAAITSCTNTSNPRNV 420
Query: 421 IAAALLARNANARGLARKPWVKSSLAPGSKAVELYLEEANLLPDLEKLGFGIVAFACTTC 480
+AA LLA+ AN GL RKPWVKSS APGSK LYLEEA LLP+LEKLGFGIVA+ACTTC
Sbjct: 421 VAAGLLAKKANELGLVRKPWVKSSFAPGSKVARLYLEEAGLLPELEKLGFGIVAYACTTC 480
Query: 481 NGMSGALDPKIQQEIIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTI 540
NGMSGAL P+IQQEIIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGT+
Sbjct: 481 NGMSGALRPEIQQEIIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTV 540
Query: 541 RFDIEKDVLGTDQDGKPVYLKDIWPSDEEIDAIVAKSVKPEQFRKVYEPMFAITAASGES 600
RFDIEKD LG D+ G PV LKD+WPSDEEIDAIV + VKPEQF++VY PMF + ++
Sbjct: 541 RFDIEKDALGYDKAGNPVTLKDLWPSDEEIDAIVGEYVKPEQFKQVYIPMFNLDEVE-QA 599
Query: 601 VSPLYDWRPQSTYIRRPPYWEGALAGERTLKALRPLAVLGDNITTDHLSPSNAIMLNSAA 660
SPLYDWRPQSTYIRRPPYWEG +A ER LK +RPLA+L DNITTDHLSPSNAI+L+SAA
Sbjct: 600 KSPLYDWRPQSTYIRRPPYWEGNMARERGLKGMRPLAILPDNITTDHLSPSNAILLDSAA 659
Query: 661 GEYLARMGLPEEDFNSYATHRGDHLTAQRATFANPTLINEMAVVD-GQVKKGSLARIEPE 719
GEYLA+MGLPEEDFNSYATHRGDHLTAQRAT ANP L NEM + G+V +GSLARIEPE
Sbjct: 660 GEYLAKMGLPEEDFNSYATHRGDHLTAQRATLANPKLFNEMVRDEKGEVIQGSLARIEPE 719
Query: 720 GKVVRMWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEVIVAEGFERIHRT 779
GKV RMWEAIETYM+R QPLI+IAGADYGQGSSRDWAAKGV LAGVE IVAEGFERIHRT
Sbjct: 720 GKVTRMWEAIETYMERGQPLIVIAGADYGQGSSRDWAAKGVALAGVEAIVAEGFERIHRT 779
Query: 780 NLIGMGVLPLEFKPGVNRLTLGLDGTETYDVIGERQPRATLTLVVNRKNGERVEVPVTCR 839
NL+GMGV+PL+F+ G R TL LDGTETYDV G+ P ATLTLV++R G VPV CR
Sbjct: 780 NLVGMGVMPLQFQEGTTRHTLKLDGTETYDVEGKPAPGATLTLVIHRAGGNSERVPVLCR 839
Query: 840 LDSDEEVSIYEAGGVL-HFAQDFLES 864
LD+ EEVS+Y AGGVL FAQDFLES
Sbjct: 840 LDTAEEVSVYSAGGVLQRFAQDFLES 865
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: 2179
Number of extensions: 80
Number of successful extensions: 4
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: 869
Length adjustment: 42
Effective length of query: 827
Effective length of database: 827
Effective search space: 683929
Effective search space used: 683929
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_086511660.1 BZY95_RS20065 (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.2572.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 1761.0 0.0 0 1760.9 0.0 1.0 1 lcl|NCBI__GCF_002151265.1:WP_086511660.1 BZY95_RS20065 Fe/S-dependent 2-m
Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_002151265.1:WP_086511660.1 BZY95_RS20065 Fe/S-dependent 2-methylisocitrate dehydratase AcnD
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1760.9 0.0 0 0 1 858 [] 2 864 .. 2 864 .. 0.99
Alignments for each domain:
== domain 1 score: 1760.9 bits; conditional E-value: 0
TIGR02333 1 ntkyrkalpgtdldyfdaraaveaikpgaydklpytsrvlaenlvrrvdpetleaslkqlierkreldf 69
nt+yrk+lpgt+ldyfd r+ave+i+pgayd+lpytsrvlae+lvrr++pe l+++lkqlier+r+ldf
lcl|NCBI__GCF_002151265.1:WP_086511660.1 2 NTQYRKPLPGTELDYFDVREAVEEIQPGAYDTLPYTSRVLAEQLVRRCEPELLTDALKQLIERRRDLDF 70
89******************************************************************* PP
TIGR02333 70 pwyparvvchdilgqtalvdlaglrdaiaekggdpaqvnpvvetqlivdhslaveyggfdpdafeknra 138
pwyparvvchdilgqtalvdlaglrdaiaekggdp++vnpvv+tqlivdhslave+gg dpdaf+knra
lcl|NCBI__GCF_002151265.1:WP_086511660.1 71 PWYPARVVCHDILGQTALVDLAGLRDAIAEKGGDPSKVNPVVPTQLIVDHSLAVECGGDDPDAFAKNRA 139
********************************************************************* PP
TIGR02333 139 iedrrnedrfhfinwtkkafknvdvipagngimhqinlekmspvvqvkegvafpdtlvgtdshtphvda 207
iedrrnedrfhfi+wt++afknvdvipagngimhqinlekmspv+q+++gva+pdt+vgtdshtph+d+
lcl|NCBI__GCF_002151265.1:WP_086511660.1 140 IEDRRNEDRFHFIDWTRTAFKNVDVIPAGNGIMHQINLEKMSPVIQARDGVAYPDTCVGTDSHTPHIDC 208
********************************************************************* PP
TIGR02333 208 lgviaigvggleaetvmlgraslmrlpdivgveltgkrqpgitatdivlalteflrkekvvsayleffg 276
lgviaigvggleaetvmlgr+s+mrlpdivgveltgkrq+gitatdivla+teflr+e+vv+ayleffg
lcl|NCBI__GCF_002151265.1:WP_086511660.1 209 LGVIAIGVGGLEAETVMLGRPSMMRLPDIVGVELTGKRQSGITATDIVLAITEFLRQERVVGAYLEFFG 277
********************************************************************* PP
TIGR02333 277 egakaltlgdratisnmtpeygataamfaideqtidylkltgreeeqvklvetyakaaglwadslkkav 345
ega +lt+gdratisnmtpeygataamf+id+qt+dyl +tgre+eqv+lve yak+ glwadslk+ +
lcl|NCBI__GCF_002151265.1:WP_086511660.1 278 EGADSLTIGDRATISNMTPEYGATAAMFYIDQQTLDYLAITGREPEQVALVENYAKTVGLWADSLKNVQ 346
********************************************************************* PP
TIGR02333 346 yervlkfdlssvvrnlagpsnpharlatsdlaakgiakevee....eaeglmpdgaviiaaitsctnts 410
yervl+fdls+v+rnlagpsnph+rl+ts la +gia ++e e g+mpdgaviiaaitsctnts
lcl|NCBI__GCF_002151265.1:WP_086511660.1 347 YERVLTFDLSTVERNLAGPSNPHRRLPTSALAERGIAVNLELalaeEKAGRMPDGAVIIAAITSCTNTS 415
*************************************998744444777******************** PP
TIGR02333 411 nprnvvaagllarnanklglkrkpwvksslapgskvvklyleeagllkeleklgfgivafacttcngms 479
nprnvvaaglla++an+lgl rkpwvkss+apgskv++lyleeagll+eleklgfgiva+acttcngms
lcl|NCBI__GCF_002151265.1:WP_086511660.1 416 NPRNVVAAGLLAKKANELGLVRKPWVKSSFAPGSKVARLYLEEAGLLPELEKLGFGIVAYACTTCNGMS 484
********************************************************************* PP
TIGR02333 480 galdpviqqeiidrdlyatavlsgnrnfdgrihpyakqaflaspplvvayaiagtirfdiekdvlgvda 548
gal p iqqeiidrdlyatavlsgnrnfdgrihpyakqaflaspplvvayaiagt+rfdiekd+lg+d+
lcl|NCBI__GCF_002151265.1:WP_086511660.1 485 GALRPEIQQEIIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTVRFDIEKDALGYDK 553
********************************************************************* PP
TIGR02333 549 dgkeirlkdiwpsdeeidavvaaavkpeqfrkvyipmfdledaqkkvsplydwrpmstyirrppywega 617
g+++ lkd+wpsdeeida+v+++vkpeqf++vyipmf+l++ +++ splydwrp+styirrppyweg
lcl|NCBI__GCF_002151265.1:WP_086511660.1 554 AGNPVTLKDLWPSDEEIDAIVGEYVKPEQFKQVYIPMFNLDEVEQAKSPLYDWRPQSTYIRRPPYWEGN 622
********************************************************************* PP
TIGR02333 618 lagertlkgmrplavlgdnittdhlspsnailldsaageylakmglpeedfnsyathrgdhltaqratf 686
+a er lkgmrpla+l+dnittdhlspsnailldsaageylakmglpeedfnsyathrgdhltaqrat+
lcl|NCBI__GCF_002151265.1:WP_086511660.1 623 MARERGLKGMRPLAILPDNITTDHLSPSNAILLDSAAGEYLAKMGLPEEDFNSYATHRGDHLTAQRATL 691
********************************************************************* PP
TIGR02333 687 anpklfnemvked.gkvkqgslariepegkvtrmweaietymnrkqpliiiagadygqgssrdwaakgv 754
anpklfnemv+++ g+v qgslariepegkvtrmweaietym+r qpli+iagadygqgssrdwaakgv
lcl|NCBI__GCF_002151265.1:WP_086511660.1 692 ANPKLFNEMVRDEkGEVIQGSLARIEPEGKVTRMWEAIETYMERGQPLIVIAGADYGQGSSRDWAAKGV 760
***********999******************************************************* PP
TIGR02333 755 rlagveaivaegferihrtnlvgmgvlplefkpgtnrktlaldgtevydvvgeitpradltlvvtrkng 823
lagveaivaegferihrtnlvgmgv+pl+f+ gt r+tl+ldgte+ydv g+ +p+a+ltlv++r+ g
lcl|NCBI__GCF_002151265.1:WP_086511660.1 761 ALAGVEAIVAEGFERIHRTNLVGMGVMPLQFQEGTTRHTLKLDGTETYDVEGKPAPGATLTLVIHRAGG 829
********************************************************************* PP
TIGR02333 824 eklevpvtcrldtaeevsvyeaggvlqrfaqdfle 858
++ vpv crldtaeevsvy aggvlqrfaqdfle
lcl|NCBI__GCF_002151265.1:WP_086511660.1 830 NSERVPVLCRLDTAEEVSVYSAGGVLQRFAQDFLE 864
*********************************97 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (858 nodes)
Target sequences: 1 (869 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 0.01s 00:00:00.06 Elapsed: 00:00:00.06
# Mc/sec: 11.11
//
[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