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_011770203.1 PING_RS09730 Fe/S-dependent 2-methylisocitrate dehydratase AcnD
Query= SwissProt::Q937N8
(869 letters)
>NCBI__GCF_000015285.1:WP_011770203.1
Length = 868
Score = 1335 bits (3456), Expect = 0.0
Identities = 664/870 (76%), Positives = 746/870 (85%), Gaps = 9/870 (1%)
Query: 1 MNSANRKPLPGTKLDYFDARAAVEAIQPGAYDKLPYTSRVLAENLVRRCDPATLTDSLLQ 60
MN RKPLPGT LDYFD R AV I+ GAY+KLPYTSRV AENLVRRC P L DSL Q
Sbjct: 1 MNDNYRKPLPGTSLDYFDTREAVNNIKKGAYEKLPYTSRVFAENLVRRCAPDKLVDSLNQ 60
Query: 61 LVGRKRDLDFPWFPARVVCHDILGQTALVDLAGLRDAIADQGGDPAKVNPVVPVQLIVDH 120
L+ RK+DLDFPW+PARVVCHDILGQTALVDLAGLRDAIA +GGDPAKVNPVVP QLIVDH
Sbjct: 61 LIERKQDLDFPWYPARVVCHDILGQTALVDLAGLRDAIALKGGDPAKVNPVVPTQLIVDH 120
Query: 121 SLAVECGGFDPDAFAKNRAIEDRRNEDRFHFIDWTKQAFKNVDVIPPGNGIMHQINLEKM 180
SLAVE GF+ DAF NR IEDRRN+DRFHFI+WTK AF+NV+VIPPGNGIMHQINLEKM
Sbjct: 121 SLAVEHAGFEKDAFELNREIEDRRNDDRFHFINWTKTAFENVEVIPPGNGIMHQINLEKM 180
Query: 181 SPVIHADNGVAYPDTCVGTDSHTPHVDALGVIAIGVGGLEAENVMLGRASWMRLPDIVGV 240
SPVI + GVA+PDT VGTDSHTPHVDALGV+A+GVGGLEAE+VMLGRAS+MR+PDIVGV
Sbjct: 181 SPVIQSREGVAFPDTLVGTDSHTPHVDALGVLALGVGGLEAESVMLGRASYMRMPDIVGV 240
Query: 241 ELTGKRQPGITATDIVLALTEFLRKEKVVGAYLEFRGEGASSLTLGDRATISNMAPEYGA 300
L GKRQ GITATDIVLA+TEFLR +KVV YLEF GEGA++LTLGDRATISNM PE+GA
Sbjct: 241 HLFGKRQEGITATDIVLAITEFLRNQKVVSCYLEFYGEGAANLTLGDRATISNMTPEFGA 300
Query: 301 TAAMFFIDEQTIDYLRLTGRTDEQLKLVETYARTAGLWADSLKNAEYERVLKFDLSSVVR 360
+A MF+ID+ TI+YL+LTGR ++Q++LVE YA+ GLWAD L NAEYERV+ FDLS+V R
Sbjct: 301 SAGMFYIDKNTIEYLKLTGRDEKQVELVENYAKQTGLWADDLVNAEYERVIDFDLSAVGR 360
Query: 361 NMAGPSNPHKRLPTSALAERGIAVDLDKASAQEAEGLMPDGAVIIAAITSCTNTSNPRNV 420
N+AGPSNPH+R+ T+ LA +GI+ + G MPDGA IIAAITSCTNTSNPRNV
Sbjct: 361 NIAGPSNPHRRVSTADLAAKGIS-----GVVENEAGKMPDGACIIAAITSCTNTSNPRNV 415
Query: 421 IAAALLARNANARGLARKPWVKSSLAPGSKAVELYLEEANLLPDLEKLGFGIVAFACTTC 480
IAAAL+ARNAN GL RKPWVK+SLAPGSK V+LYLEEANLL +LE+LGFGIV FACTTC
Sbjct: 416 IAAALVARNANKLGLTRKPWVKTSLAPGSKTVQLYLEEANLLTELEELGFGIVGFACTTC 475
Query: 481 NGMSGALDPKIQQEIIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTI 540
NGMSGALDPKIQ+E+I+RDLY TAVLSGNRNFDGRIHPYAKQAF+ASPPLVVAYAIAGTI
Sbjct: 476 NGMSGALDPKIQEEVIERDLYTTAVLSGNRNFDGRIHPYAKQAFIASPPLVVAYAIAGTI 535
Query: 541 RFDIEKDVLGTDQDGKPVYLKDIWPSDEEIDAIVAKSVKPEQFRKVYEPMFAITA---AS 597
RFDIE D LG D DG + LKDIWPSD EID I+ + VKP QF+ VYEPMF I
Sbjct: 536 RFDIENDALGIDPDGNKITLKDIWPSDAEIDEIITQCVKPAQFKAVYEPMFDIKVDYDEE 595
Query: 598 GESVSPLYDWRPQSTYIRRPPYWEGALAGERTLKALRPLAVLGDNITTDHLSPSNAIMLN 657
E +SP+YDWRP+STYIRRPPYW GALAGERTLK +RPLAVLGDNITTDHLSPSNAIML+
Sbjct: 596 LEKISPVYDWRPESTYIRRPPYWSGALAGERTLKNMRPLAVLGDNITTDHLSPSNAIMLD 655
Query: 658 SAAGEYLARMGLPEEDFNSYATHRGDHLTAQRATFANPTLINEMAVVDGQVKKGSLARIE 717
SAAG YL +MGLPE DFNSYATHRGDHLTAQRATFANP L NEM DG++++GSLAR+E
Sbjct: 656 SAAGAYLDKMGLPEVDFNSYATHRGDHLTAQRATFANPKLFNEMVKKDGEIQQGSLARVE 715
Query: 718 PEGKVVRMWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEVIVAEGFERIH 777
PEG V+RMWEAIE YM RKQPLII+AGADYGQGSSRDWAAKGVRLAGVEVIVAEGFERIH
Sbjct: 716 PEGNVMRMWEAIEIYMARKQPLIIVAGADYGQGSSRDWAAKGVRLAGVEVIVAEGFERIH 775
Query: 778 RTNLIGMGVLPLEFKPGVNRLTLGLDGTETYDVIGERQPRATLTLVVNRKNGERVEVPVT 837
RTNL+GMGVLP+EF NR T +DGTET+DVIG+ P A LTL++NR +GE + V V
Sbjct: 776 RTNLVGMGVLPVEFINAENRHTYAIDGTETFDVIGKPTPGALLTLIINRPSGETINVEVK 835
Query: 838 CRLDSDEEVSIYEAGGVL-HFAQDFLESSR 866
CRLD++EEVSIYEAGG+L FAQDF+ESS+
Sbjct: 836 CRLDTEEEVSIYEAGGILQRFAQDFIESSK 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: 2157
Number of extensions: 93
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: 868
Length adjustment: 42
Effective length of query: 827
Effective length of database: 826
Effective search space: 683102
Effective search space used: 683102
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_011770203.1 PING_RS09730 (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.4018714.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 1718.7 0.0 0 1718.6 0.0 1.0 1 NCBI__GCF_000015285.1:WP_011770203.1
Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000015285.1:WP_011770203.1
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1718.6 0.0 0 0 1 858 [] 2 862 .. 2 862 .. 0.99
Alignments for each domain:
== domain 1 score: 1718.6 bits; conditional E-value: 0
TIGR02333 1 ntkyrkalpgtdldyfdaraaveaikpgaydklpytsrvlaenlvrrvdpetleaslkqlierkreldfpwyp 73
n +yrk+lpgt+ldyfd+r+av++ik gay+klpytsrv+aenlvrr+ p++l +sl+qlierk++ldfpwyp
NCBI__GCF_000015285.1:WP_011770203.1 2 NDNYRKPLPGTSLDYFDTREAVNNIKKGAYEKLPYTSRVFAENLVRRCAPDKLVDSLNQLIERKQDLDFPWYP 74
789********************************************************************** PP
TIGR02333 74 arvvchdilgqtalvdlaglrdaiaekggdpaqvnpvvetqlivdhslaveyggfdpdafeknraiedrrned 146
arvvchdilgqtalvdlaglrdaia kggdpa+vnpvv+tqlivdhslave +gf++dafe nr+iedrrn+d
NCBI__GCF_000015285.1:WP_011770203.1 75 ARVVCHDILGQTALVDLAGLRDAIALKGGDPAKVNPVVPTQLIVDHSLAVEHAGFEKDAFELNREIEDRRNDD 147
************************************************************************* PP
TIGR02333 147 rfhfinwtkkafknvdvipagngimhqinlekmspvvqvkegvafpdtlvgtdshtphvdalgviaigvggle 219
rfhfinwtk+af+nv+vip+gngimhqinlekmspv+q++egvafpdtlvgtdshtphvdalgv+a+gvggle
NCBI__GCF_000015285.1:WP_011770203.1 148 RFHFINWTKTAFENVEVIPPGNGIMHQINLEKMSPVIQSREGVAFPDTLVGTDSHTPHVDALGVLALGVGGLE 220
************************************************************************* PP
TIGR02333 220 aetvmlgraslmrlpdivgveltgkrqpgitatdivlalteflrkekvvsayleffgegakaltlgdratisn 292
ae+vmlgras+mr+pdivgv+l gkrq gitatdivla+teflr++kvvs+ylef+gega ltlgdratisn
NCBI__GCF_000015285.1:WP_011770203.1 221 AESVMLGRASYMRMPDIVGVHLFGKRQEGITATDIVLAITEFLRNQKVVSCYLEFYGEGAANLTLGDRATISN 293
************************************************************************* PP
TIGR02333 293 mtpeygataamfaideqtidylkltgreeeqvklvetyakaaglwadslkkavyervlkfdlssvvrnlagps 365
mtpe+ga+a+mf+id++ti+ylkltgr+e+qv+lve yak +glwad+l +a+yerv++fdls+v rn+agps
NCBI__GCF_000015285.1:WP_011770203.1 294 MTPEFGASAGMFYIDKNTIEYLKLTGRDEKQVELVENYAKQTGLWADDLVNAEYERVIDFDLSAVGRNIAGPS 366
************************************************************************* PP
TIGR02333 366 npharlatsdlaakgiakeveeeaeglmpdgaviiaaitsctntsnprnvvaagllarnanklglkrkpwvks 438
nph+r++t+dlaakgi++ ve+ea g+mpdga iiaaitsctntsnprnv+aa+l+arnanklgl+rkpwvk+
NCBI__GCF_000015285.1:WP_011770203.1 367 NPHRRVSTADLAAKGISGVVENEA-GKMPDGACIIAAITSCTNTSNPRNVIAAALVARNANKLGLTRKPWVKT 438
***********************9.************************************************ PP
TIGR02333 439 slapgskvvklyleeagllkeleklgfgivafacttcngmsgaldpviqqeiidrdlyatavlsgnrnfdgri 511
slapgsk+v+lyleea+ll+ele+lgfgiv+facttcngmsgaldp+iq+e+i+rdly+tavlsgnrnfdgri
NCBI__GCF_000015285.1:WP_011770203.1 439 SLAPGSKTVQLYLEEANLLTELEELGFGIVGFACTTCNGMSGALDPKIQEEVIERDLYTTAVLSGNRNFDGRI 511
************************************************************************* PP
TIGR02333 512 hpyakqaflaspplvvayaiagtirfdiekdvlgvdadgkeirlkdiwpsdeeidavvaaavkpeqfrkvyip 584
hpyakqaf+aspplvvayaiagtirfdie+d+lg+d dg++i lkdiwpsd+eid ++++ vkp qf+ vy+p
NCBI__GCF_000015285.1:WP_011770203.1 512 HPYAKQAFIASPPLVVAYAIAGTIRFDIENDALGIDPDGNKITLKDIWPSDAEIDEIITQCVKPAQFKAVYEP 584
************************************************************************* PP
TIGR02333 585 mfdle....daqkkvsplydwrpmstyirrppywegalagertlkgmrplavlgdnittdhlspsnailldsa 653
mfd++ ++ +k sp+ydwrp styirrppyw galagertlk mrplavlgdnittdhlspsnai+ldsa
NCBI__GCF_000015285.1:WP_011770203.1 585 MFDIKvdydEELEKISPVYDWRPESTYIRRPPYWSGALAGERTLKNMRPLAVLGDNITTDHLSPSNAIMLDSA 657
**9977232445799********************************************************** PP
TIGR02333 654 ageylakmglpeedfnsyathrgdhltaqratfanpklfnemvkedgkvkqgslariepegkvtrmweaiety 726
ag yl kmglpe dfnsyathrgdhltaqratfanpklfnemvk+dg+++qgslar+epeg+v+rmweaie y
NCBI__GCF_000015285.1:WP_011770203.1 658 AGAYLDKMGLPEVDFNSYATHRGDHLTAQRATFANPKLFNEMVKKDGEIQQGSLARVEPEGNVMRMWEAIEIY 730
************************************************************************* PP
TIGR02333 727 mnrkqpliiiagadygqgssrdwaakgvrlagveaivaegferihrtnlvgmgvlplefkpgtnrktlaldgt 799
m rkqplii+agadygqgssrdwaakgvrlagve ivaegferihrtnlvgmgvlp+ef + +nr+t+a+dgt
NCBI__GCF_000015285.1:WP_011770203.1 731 MARKQPLIIVAGADYGQGSSRDWAAKGVRLAGVEVIVAEGFERIHRTNLVGMGVLPVEFINAENRHTYAIDGT 803
************************************************************************* PP
TIGR02333 800 evydvvgeitpradltlvvtrkngeklevpvtcrldtaeevsvyeaggvlqrfaqdfle 858
e++dv+g+ tp+a ltl+++r ge+++v v crldt eevs+yeagg+lqrfaqdf+e
NCBI__GCF_000015285.1:WP_011770203.1 804 ETFDVIGKPTPGALLTLIINRPSGETINVEVKCRLDTEEEVSIYEAGGILQRFAQDFIE 862
*********************************************************86 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (858 nodes)
Target sequences: 1 (868 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: 24.87
//
[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