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_036138977.1 N800_RS12170 Fe/S-dependent 2-methylisocitrate dehydratase AcnD
Query= SwissProt::Q937N8
(869 letters)
>NCBI__GCF_000768355.1:WP_036138977.1
Length = 869
Score = 1476 bits (3820), Expect = 0.0
Identities = 735/869 (84%), Positives = 797/869 (91%), Gaps = 3/869 (0%)
Query: 1 MNSANRKPLPGTKLDYFDARAAVEAIQPGAYDKLPYTSRVLAENLVRRCDPATLTDSLLQ 60
MN+A+RKPLPGTKLD+FDAR AVEA+QPGA+ LPYT+RV AEN+VR+ DPA L Q
Sbjct: 1 MNNAHRKPLPGTKLDWFDAREAVEALQPGAWATLPYTARVHAENIVRKADPAMRDAYLRQ 60
Query: 61 LVGRKRDLDFPWFPARVVCHDILGQTALVDLAGLRDAIADQGGDPAKVNPVVPVQLIVDH 120
LV R+RDLDFPWFPARVVCHDILGQTALVDLAGLRDAIAD+GGDPA+VNPVVPVQLIVDH
Sbjct: 61 LVERRRDLDFPWFPARVVCHDILGQTALVDLAGLRDAIADKGGDPAQVNPVVPVQLIVDH 120
Query: 121 SLAVECGGFDPDAFAKNRAIEDRRNEDRFHFIDWTKQAFKNVDVIPPGNGIMHQINLEKM 180
SLAVECGGFDPDAFAKNRAIEDRRNEDRFHFIDWTKQAF+NVDVIPPGNGIMHQINLEKM
Sbjct: 121 SLAVECGGFDPDAFAKNRAIEDRRNEDRFHFIDWTKQAFRNVDVIPPGNGIMHQINLEKM 180
Query: 181 SPVIHADNGVAYPDTCVGTDSHTPHVDALGVIAIGVGGLEAENVMLGRASWMRLPDIVGV 240
SPVI+ +GVA+PDTCVGTDSHTPHVDALGVIA+GVGGLEAENVMLGRASWMRLPDIVGV
Sbjct: 181 SPVIYVQDGVAFPDTCVGTDSHTPHVDALGVIAVGVGGLEAENVMLGRASWMRLPDIVGV 240
Query: 241 ELTGKRQPGITATDIVLALTEFLRKEKVVGAYLEFRGEGASSLTLGDRATISNMAPEYGA 300
ELTGK QPGITATDIVL+LTEFLRK+KVVGAYLEFRGEGA++LT+GDRATISNMAPEYGA
Sbjct: 241 ELTGKPQPGITATDIVLSLTEFLRKQKVVGAYLEFRGEGAAALTIGDRATISNMAPEYGA 300
Query: 301 TAAMFFIDEQTIDYLRLTGRTDEQLKLVETYARTAGLWADSLKNAEYERVLKFDLSSVVR 360
TAAMFFID+ T+DYLRLTGR+DEQ+ LVETYA+ AGLWAD L+ A+YER L FDLSSV R
Sbjct: 301 TAAMFFIDDNTLDYLRLTGRSDEQVALVETYAKAAGLWADDLRTAQYERTLHFDLSSVER 360
Query: 361 NMAGPSNPHKRLPTSALAERGIAVDLDKASAQEAEGLMPDGAVIIAAITSCTNTSNPRNV 420
MAGPSNPH RLP + LAERGIA +L+ A AQEA+GL+PDGAVIIAAITSCTNTSNPRNV
Sbjct: 361 TMAGPSNPHARLPVAQLAERGIAGNLEAARAQEAQGLLPDGAVIIAAITSCTNTSNPRNV 420
Query: 421 IAAALLARNANARGLARKPWVKSSLAPGSKAVELYLEEANLLPDLEKLGFGIVAFACTTC 480
IAA LLARNA GL RKPWVK+SLAPGSKAV LYL+EA L DLE+LGFGIVAFACTTC
Sbjct: 421 IAAGLLARNAARLGLQRKPWVKTSLAPGSKAVALYLDEAGLTDDLEQLGFGIVAFACTTC 480
Query: 481 NGMSGALDPKIQQEIIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTI 540
NGMSGALDPKIQQEIIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTI
Sbjct: 481 NGMSGALDPKIQQEIIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTI 540
Query: 541 RFDIEKDVLGTDQDGKPVYLKDIWPSDEEIDAIVAKSVKPEQFRKVYEPMFAITAASGES 600
RFDIEKDVLG DG+ + LKD+WP+D EIDA++ +VKPEQFRKVYEPMF + G +
Sbjct: 541 RFDIEKDVLGV-VDGREIRLKDLWPTDAEIDAVMKAAVKPEQFRKVYEPMFNVRVEHGGA 599
Query: 601 VSPLYDWRPQSTYIRRPPYWEGALAGERTLKALRPLAVLGDNITTDHLSPSNAIMLNSAA 660
VSPLYDWRPQSTYIRRPPYWEGALAGERTL+ +RPLAVLGDNITTDHLSPSNAI+L+SAA
Sbjct: 600 VSPLYDWRPQSTYIRRPPYWEGALAGERTLRGMRPLAVLGDNITTDHLSPSNAILLDSAA 659
Query: 661 GEYLARMGLPEEDFNSYATHRGDHLTAQRATFANPTLINEMA-VVDGQVKKGSLARIEPE 719
GEYL +MGLPEEDFNSYATHRGDHLTAQRATFANP L NEM DG V++GSLARIEPE
Sbjct: 660 GEYLDKMGLPEEDFNSYATHRGDHLTAQRATFANPKLFNEMVRKDDGSVRQGSLARIEPE 719
Query: 720 GKVVRMWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEVIVAEGFERIHRT 779
G+V RMWEAIETYM+RKQPLIIIAGADYGQGSSRDWAAKGVRLAGVE IVAEGFERIHRT
Sbjct: 720 GQVTRMWEAIETYMERKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEAIVAEGFERIHRT 779
Query: 780 NLIGMGVLPLEFKPGVNRLTLGLDGTETYDVIGERQPRATLTLVVNRKNGERVEVPVTCR 839
NLIGMGVLPLEF+PG +R TL +DGTETYDVIGER PRATLTLV++R+NGERVEVPVTCR
Sbjct: 780 NLIGMGVLPLEFQPGADRTTLAIDGTETYDVIGERTPRATLTLVIHRRNGERVEVPVTCR 839
Query: 840 LDSDEEVSIYEAGGVL-HFAQDFLESSRA 867
LD+ EEVSIYEAGGVL FA DFLESS+A
Sbjct: 840 LDTAEEVSIYEAGGVLQRFANDFLESSKA 868
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: 2275
Number of extensions: 89
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_036138977.1 N800_RS12170 (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.494971.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 1789.7 0.1 0 1789.5 0.1 1.0 1 NCBI__GCF_000768355.1:WP_036138977.1
Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000768355.1:WP_036138977.1
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1789.5 0.1 0 0 1 858 [] 2 864 .. 2 864 .. 0.99
Alignments for each domain:
== domain 1 score: 1789.5 bits; conditional E-value: 0
TIGR02333 1 ntkyrkalpgtdldyfdaraaveaikpgaydklpytsrvlaenlvrrvdpetleaslkqlierkreldfpwyp 73
n+++rk+lpgt+ld+fdar+avea++pga+++lpyt+rv aen+vr++dp++ +a+l+ql+er+r+ldfpw+p
NCBI__GCF_000768355.1:WP_036138977.1 2 NNAHRKPLPGTKLDWFDAREAVEALQPGAWATLPYTARVHAENIVRKADPAMRDAYLRQLVERRRDLDFPWFP 74
7889********************************************************************* PP
TIGR02333 74 arvvchdilgqtalvdlaglrdaiaekggdpaqvnpvvetqlivdhslaveyggfdpdafeknraiedrrned 146
arvvchdilgqtalvdlaglrdaia+kggdpaqvnpvv++qlivdhslave+ggfdpdaf+knraiedrrned
NCBI__GCF_000768355.1:WP_036138977.1 75 ARVVCHDILGQTALVDLAGLRDAIADKGGDPAQVNPVVPVQLIVDHSLAVECGGFDPDAFAKNRAIEDRRNED 147
************************************************************************* PP
TIGR02333 147 rfhfinwtkkafknvdvipagngimhqinlekmspvvqvkegvafpdtlvgtdshtphvdalgviaigvggle 219
rfhfi+wtk+af+nvdvip+gngimhqinlekmspv+ v++gvafpdt+vgtdshtphvdalgvia+gvggle
NCBI__GCF_000768355.1:WP_036138977.1 148 RFHFIDWTKQAFRNVDVIPPGNGIMHQINLEKMSPVIYVQDGVAFPDTCVGTDSHTPHVDALGVIAVGVGGLE 220
************************************************************************* PP
TIGR02333 220 aetvmlgraslmrlpdivgveltgkrqpgitatdivlalteflrkekvvsayleffgegakaltlgdratisn 292
ae+vmlgras+mrlpdivgveltgk qpgitatdivl+lteflrk+kvv+aylef gega alt+gdratisn
NCBI__GCF_000768355.1:WP_036138977.1 221 AENVMLGRASWMRLPDIVGVELTGKPQPGITATDIVLSLTEFLRKQKVVGAYLEFRGEGAAALTIGDRATISN 293
************************************************************************* PP
TIGR02333 293 mtpeygataamfaideqtidylkltgreeeqvklvetyakaaglwadslkkavyervlkfdlssvvrnlagps 365
m+peygataamf+id++t+dyl+ltgr +eqv+lvetyakaaglwad+l++a+yer+l+fdlssv+r++agps
NCBI__GCF_000768355.1:WP_036138977.1 294 MAPEYGATAAMFFIDDNTLDYLRLTGRSDEQVALVETYAKAAGLWADDLRTAQYERTLHFDLSSVERTMAGPS 366
************************************************************************* PP
TIGR02333 366 npharlatsdlaakgiakevee....eaeglmpdgaviiaaitsctntsnprnvvaagllarnanklglkrkp 434
npharl+ ++la +gia+++e ea+gl+pdgaviiaaitsctntsnprnv+aagllarna +lgl+rkp
NCBI__GCF_000768355.1:WP_036138977.1 367 NPHARLPVAQLAERGIAGNLEAaraqEAQGLLPDGAVIIAAITSCTNTSNPRNVIAAGLLARNAARLGLQRKP 439
******************99866666899******************************************** PP
TIGR02333 435 wvksslapgskvvklyleeagllkeleklgfgivafacttcngmsgaldpviqqeiidrdlyatavlsgnrnf 507
wvk+slapgsk+v lyl+eagl ++le+lgfgivafacttcngmsgaldp+iqqeiidrdlyatavlsgnrnf
NCBI__GCF_000768355.1:WP_036138977.1 440 WVKTSLAPGSKAVALYLDEAGLTDDLEQLGFGIVAFACTTCNGMSGALDPKIQQEIIDRDLYATAVLSGNRNF 512
************************************************************************* PP
TIGR02333 508 dgrihpyakqaflaspplvvayaiagtirfdiekdvlgvdadgkeirlkdiwpsdeeidavvaaavkpeqfrk 580
dgrihpyakqaflaspplvvayaiagtirfdiekdvlgv +dg+eirlkd+wp+d+eidav++aavkpeqfrk
NCBI__GCF_000768355.1:WP_036138977.1 513 DGRIHPYAKQAFLASPPLVVAYAIAGTIRFDIEKDVLGV-VDGREIRLKDLWPTDAEIDAVMKAAVKPEQFRK 584
***************************************.********************************* PP
TIGR02333 581 vyipmfdle.daqkkvsplydwrpmstyirrppywegalagertlkgmrplavlgdnittdhlspsnaillds 652
vy+pmf++ +++ +vsplydwrp+styirrppywegalagertl+gmrplavlgdnittdhlspsnaillds
NCBI__GCF_000768355.1:WP_036138977.1 585 VYEPMFNVRvEHGGAVSPLYDWRPQSTYIRRPPYWEGALAGERTLRGMRPLAVLGDNITTDHLSPSNAILLDS 657
*********9*************************************************************** PP
TIGR02333 653 aageylakmglpeedfnsyathrgdhltaqratfanpklfnemvked.gkvkqgslariepegkvtrmweaie 724
aageyl kmglpeedfnsyathrgdhltaqratfanpklfnemv++d g+v+qgslariepeg+vtrmweaie
NCBI__GCF_000768355.1:WP_036138977.1 658 AAGEYLDKMGLPEEDFNSYATHRGDHLTAQRATFANPKLFNEMVRKDdGSVRQGSLARIEPEGQVTRMWEAIE 730
********************************************9988************************* PP
TIGR02333 725 tymnrkqpliiiagadygqgssrdwaakgvrlagveaivaegferihrtnlvgmgvlplefkpgtnrktlald 797
tym+rkqpliiiagadygqgssrdwaakgvrlagveaivaegferihrtnl+gmgvlplef+pg++r+tla+d
NCBI__GCF_000768355.1:WP_036138977.1 731 TYMERKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEAIVAEGFERIHRTNLIGMGVLPLEFQPGADRTTLAID 803
************************************************************************* PP
TIGR02333 798 gtevydvvgeitpradltlvvtrkngeklevpvtcrldtaeevsvyeaggvlqrfaqdfle 858
gte+ydv+ge+tpra+ltlv++r+nge++evpvtcrldtaeevs+yeaggvlqrfa+dfle
NCBI__GCF_000768355.1:WP_036138977.1 804 GTETYDVIGERTPRATLTLVIHRRNGERVEVPVTCRLDTAEEVSIYEAGGVLQRFANDFLE 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 33.31
//
[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