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_028487612.1 Q394_RS0100860 Fe/S-dependent 2-methylisocitrate dehydratase AcnD
Query= SwissProt::Q937N8
(869 letters)
>NCBI__GCF_000621325.1:WP_028487612.1
Length = 867
Score = 1433 bits (3709), Expect = 0.0
Identities = 712/868 (82%), Positives = 777/868 (89%), Gaps = 2/868 (0%)
Query: 1 MNSANRKPLPGTKLDYFDARAAVEAIQPGAYDKLPYTSRVLAENLVRRCDPATLTDSLLQ 60
MN+ RK LPGTKLDYFD RAA+EAIQPG+Y LPYTSRVLAE LVRRC+P LTDSL Q
Sbjct: 1 MNTEYRKNLPGTKLDYFDTRAAIEAIQPGSYATLPYTSRVLAEQLVRRCEPEMLTDSLKQ 60
Query: 61 LVGRKRDLDFPWFPARVVCHDILGQTALVDLAGLRDAIADQGGDPAKVNPVVPVQLIVDH 120
L+ K+DLDFPW+PARVVCHDILGQTALVDLAGLRDAIADQGG+PAKVNPVVP QLIVDH
Sbjct: 61 LIEGKQDLDFPWYPARVVCHDILGQTALVDLAGLRDAIADQGGNPAKVNPVVPTQLIVDH 120
Query: 121 SLAVECGGFDPDAFAKNRAIEDRRNEDRFHFIDWTKQAFKNVDVIPPGNGIMHQINLEKM 180
SLAVECGGFDPDAFAKNRAIEDRRNEDRFHFI+WTK AFKNVDVIP GNGIMHQINLEKM
Sbjct: 121 SLAVECGGFDPDAFAKNRAIEDRRNEDRFHFIEWTKTAFKNVDVIPAGNGIMHQINLEKM 180
Query: 181 SPVIHADNGVAYPDTCVGTDSHTPHVDALGVIAIGVGGLEAENVMLGRASWMRLPDIVGV 240
SPVI A +GVA+PDTCVGTDSHTPHVDALGVIAIGVGGLEAE VMLG S MRLPDI+GV
Sbjct: 181 SPVIQARDGVAFPDTCVGTDSHTPHVDALGVIAIGVGGLEAETVMLGLPSMMRLPDIIGV 240
Query: 241 ELTGKRQPGITATDIVLALTEFLRKEKVVGAYLEFRGEGASSLTLGDRATISNMAPEYGA 300
+L GKRQPGITATDIVLA+TEFLRKE+VV A+LEF GEGA +LT+GDRATISNM PE+GA
Sbjct: 241 KLVGKRQPGITATDIVLAITEFLRKERVVSAWLEFFGEGAKNLTIGDRATISNMTPEFGA 300
Query: 301 TAAMFFIDEQTIDYLRLTGRTDEQLKLVETYARTAGLWADSLKNAEYERVLKFDLSSVVR 360
+A MF+IDEQTIDYL+LTGR EQ+ LVE YA+ GLWADSL +A Y RVL+FDLSSVVR
Sbjct: 301 SAGMFYIDEQTIDYLKLTGREPEQVALVENYAKATGLWADSLVDATYPRVLEFDLSSVVR 360
Query: 361 NMAGPSNPHKRLPTSALAERGIAVDLDKASAQEAEGLMPDGAVIIAAITSCTNTSNPRNV 420
NMAGPSNPH+RLPT+ LAERGIAV+L A A+EAEG MPDGAVIIAAITSCTNTSNPRNV
Sbjct: 361 NMAGPSNPHRRLPTADLAERGIAVNLAAAQAEEAEGKMPDGAVIIAAITSCTNTSNPRNV 420
Query: 421 IAAALLARNANARGLARKPWVKSSLAPGSKAVELYLEEANLLPDLEKLGFGIVAFACTTC 480
+AAALLARNAN GL RKPWVK+S APGSK ELYL+EA LL +LE+LGFGIV FACTTC
Sbjct: 421 VAAALLARNANKLGLVRKPWVKTSFAPGSKVAELYLQEAGLLTELEQLGFGIVGFACTTC 480
Query: 481 NGMSGALDPKIQQEIIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTI 540
NGMSGALDP IQQEIIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTI
Sbjct: 481 NGMSGALDPVIQQEIIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTI 540
Query: 541 RFDIEKDVLGTDQDGKPVYLKDIWPSDEEIDAIVAKSVKPEQFRKVYEPMFAITAASGES 600
RFDIEKDVLGTD+DG P+ LKDIWP+DEEIDAIVA SVKPEQF+++Y PMF + E+
Sbjct: 541 RFDIEKDVLGTDKDGNPITLKDIWPTDEEIDAIVATSVKPEQFKQIYIPMFDLGTVE-EA 599
Query: 601 VSPLYDWRPQSTYIRRPPYWEGALAGERTLKALRPLAVLGDNITTDHLSPSNAIMLNSAA 660
SPLYDWRP STYIRRPPYWEGALAGERTLK + PLAVL DNITTDHLSPSNAIM+NSAA
Sbjct: 600 KSPLYDWRPMSTYIRRPPYWEGALAGERTLKGMLPLAVLPDNITTDHLSPSNAIMMNSAA 659
Query: 661 GEYLARMGLPEEDFNSYATHRGDHLTAQRATFANPTLINEMAVVDGQVKKGSLARIEPEG 720
GEYL +MGLPEEDFNSYATHRGDHLTAQRATFANP LINEMAVVDG+VK+GSLAR+EPEG
Sbjct: 660 GEYLHKMGLPEEDFNSYATHRGDHLTAQRATFANPKLINEMAVVDGKVKQGSLARVEPEG 719
Query: 721 KVVRMWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEVIVAEGFERIHRTN 780
+V+RMWEAIETYM+RKQPLII+AGADYGQGSSRDWAAKGVRLAGVE IVAEGFERIHRTN
Sbjct: 720 QVMRMWEAIETYMERKQPLIIVAGADYGQGSSRDWAAKGVRLAGVEAIVAEGFERIHRTN 779
Query: 781 LIGMGVLPLEFKPGVNRLTLGLDGTETYDVIGERQPRATLTLVVNRKNGERVEVPVTCRL 840
L+GMGVLPLEFK G R T +DGTE+YDV G+ PR LT++++R+NGE V +PVTCRL
Sbjct: 780 LVGMGVLPLEFKAGETRKTYAIDGTESYDVEGDIAPRTDLTVIMHRRNGETVRIPVTCRL 839
Query: 841 DSDEEVSIYEAGGVL-HFAQDFLESSRA 867
D+ EV +Y AGGVL FAQDFLE A
Sbjct: 840 DTAAEVRVYNAGGVLQRFAQDFLEGDAA 867
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: 2209
Number of extensions: 86
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: 867
Length adjustment: 42
Effective length of query: 827
Effective length of database: 825
Effective search space: 682275
Effective search space used: 682275
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_028487612.1 Q394_RS0100860 (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.2786403.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 1814.4 0.1 0 1814.3 0.1 1.0 1 NCBI__GCF_000621325.1:WP_028487612.1
Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000621325.1:WP_028487612.1
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1814.3 0.1 0 0 1 858 [] 2 863 .. 2 863 .. 0.99
Alignments for each domain:
== domain 1 score: 1814.3 bits; conditional E-value: 0
TIGR02333 1 ntkyrkalpgtdldyfdaraaveaikpgaydklpytsrvlaenlvrrvdpetleaslkqlierkreldfpwyp 73
nt+yrk+lpgt+ldyfd+raa+eai+pg+y++lpytsrvlae+lvrr++pe+l++slkqlie+k++ldfpwyp
NCBI__GCF_000621325.1:WP_028487612.1 2 NTEYRKNLPGTKLDYFDTRAAIEAIQPGSYATLPYTSRVLAEQLVRRCEPEMLTDSLKQLIEGKQDLDFPWYP 74
899********************************************************************** PP
TIGR02333 74 arvvchdilgqtalvdlaglrdaiaekggdpaqvnpvvetqlivdhslaveyggfdpdafeknraiedrrned 146
arvvchdilgqtalvdlaglrdaia++gg+pa+vnpvv+tqlivdhslave+ggfdpdaf+knraiedrrned
NCBI__GCF_000621325.1:WP_028487612.1 75 ARVVCHDILGQTALVDLAGLRDAIADQGGNPAKVNPVVPTQLIVDHSLAVECGGFDPDAFAKNRAIEDRRNED 147
************************************************************************* PP
TIGR02333 147 rfhfinwtkkafknvdvipagngimhqinlekmspvvqvkegvafpdtlvgtdshtphvdalgviaigvggle 219
rfhfi+wtk+afknvdvipagngimhqinlekmspv+q+++gvafpdt+vgtdshtphvdalgviaigvggle
NCBI__GCF_000621325.1:WP_028487612.1 148 RFHFIEWTKTAFKNVDVIPAGNGIMHQINLEKMSPVIQARDGVAFPDTCVGTDSHTPHVDALGVIAIGVGGLE 220
************************************************************************* PP
TIGR02333 220 aetvmlgraslmrlpdivgveltgkrqpgitatdivlalteflrkekvvsayleffgegakaltlgdratisn 292
aetvmlg +s+mrlpdi+gv+l gkrqpgitatdivla+teflrke+vvsa+leffgegak lt+gdratisn
NCBI__GCF_000621325.1:WP_028487612.1 221 AETVMLGLPSMMRLPDIIGVKLVGKRQPGITATDIVLAITEFLRKERVVSAWLEFFGEGAKNLTIGDRATISN 293
************************************************************************* PP
TIGR02333 293 mtpeygataamfaideqtidylkltgreeeqvklvetyakaaglwadslkkavyervlkfdlssvvrnlagps 365
mtpe+ga+a+mf+ideqtidylkltgre+eqv+lve yaka+glwadsl +a y+rvl+fdlssvvrn+agps
NCBI__GCF_000621325.1:WP_028487612.1 294 MTPEFGASAGMFYIDEQTIDYLKLTGREPEQVALVENYAKATGLWADSLVDATYPRVLEFDLSSVVRNMAGPS 366
************************************************************************* PP
TIGR02333 366 npharlatsdlaakgiakevee....eaeglmpdgaviiaaitsctntsnprnvvaagllarnanklglkrkp 434
nph+rl+t+dla +gia ++ eaeg+mpdgaviiaaitsctntsnprnvvaa+llarnanklgl rkp
NCBI__GCF_000621325.1:WP_028487612.1 367 NPHRRLPTADLAERGIAVNLAAaqaeEAEGKMPDGAVIIAAITSCTNTSNPRNVVAAALLARNANKLGLVRKP 439
****************987543333499********************************************* PP
TIGR02333 435 wvksslapgskvvklyleeagllkeleklgfgivafacttcngmsgaldpviqqeiidrdlyatavlsgnrnf 507
wvk+s+apgskv++lyl+eagll+ele+lgfgiv+facttcngmsgaldpviqqeiidrdlyatavlsgnrnf
NCBI__GCF_000621325.1:WP_028487612.1 440 WVKTSFAPGSKVAELYLQEAGLLTELEQLGFGIVGFACTTCNGMSGALDPVIQQEIIDRDLYATAVLSGNRNF 512
************************************************************************* PP
TIGR02333 508 dgrihpyakqaflaspplvvayaiagtirfdiekdvlgvdadgkeirlkdiwpsdeeidavvaaavkpeqfrk 580
dgrihpyakqaflaspplvvayaiagtirfdiekdvlg+d+dg++i lkdiwp+deeida+va++vkpeqf++
NCBI__GCF_000621325.1:WP_028487612.1 513 DGRIHPYAKQAFLASPPLVVAYAIAGTIRFDIEKDVLGTDKDGNPITLKDIWPTDEEIDAIVATSVKPEQFKQ 585
************************************************************************* PP
TIGR02333 581 vyipmfdledaqkkvsplydwrpmstyirrppywegalagertlkgmrplavlgdnittdhlspsnailldsa 653
+yipmfdl++ +++ splydwrpmstyirrppywegalagertlkgm plavl+dnittdhlspsnai+++sa
NCBI__GCF_000621325.1:WP_028487612.1 586 IYIPMFDLGTVEEAKSPLYDWRPMSTYIRRPPYWEGALAGERTLKGMLPLAVLPDNITTDHLSPSNAIMMNSA 658
************************************************************************* PP
TIGR02333 654 ageylakmglpeedfnsyathrgdhltaqratfanpklfnemvkedgkvkqgslariepegkvtrmweaiety 726
ageyl+kmglpeedfnsyathrgdhltaqratfanpkl+nem+ +dgkvkqgslar+epeg+v+rmweaiety
NCBI__GCF_000621325.1:WP_028487612.1 659 AGEYLHKMGLPEEDFNSYATHRGDHLTAQRATFANPKLINEMAVVDGKVKQGSLARVEPEGQVMRMWEAIETY 731
************************************************************************* PP
TIGR02333 727 mnrkqpliiiagadygqgssrdwaakgvrlagveaivaegferihrtnlvgmgvlplefkpgtnrktlaldgt 799
m+rkqplii+agadygqgssrdwaakgvrlagveaivaegferihrtnlvgmgvlplefk+g+ rkt+a+dgt
NCBI__GCF_000621325.1:WP_028487612.1 732 MERKQPLIIVAGADYGQGSSRDWAAKGVRLAGVEAIVAEGFERIHRTNLVGMGVLPLEFKAGETRKTYAIDGT 804
************************************************************************* PP
TIGR02333 800 evydvvgeitpradltlvvtrkngeklevpvtcrldtaeevsvyeaggvlqrfaqdfle 858
e ydv g+i+pr+dlt++++r+nge++ +pvtcrldta ev+vy+aggvlqrfaqdfle
NCBI__GCF_000621325.1:WP_028487612.1 805 ESYDVEGDIAPRTDLTVIMHRRNGETVRIPVTCRLDTAAEVRVYNAGGVLQRFAQDFLE 863
*********************************************************97 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (858 nodes)
Target sequences: 1 (867 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 29.47
//
[ok]
This GapMind analysis is from Apr 09 2024. 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