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_054342411.1 Nant_RS14685 Fe/S-dependent 2-methylisocitrate dehydratase AcnD
Query= SwissProt::Q937N8
(869 letters)
>NCBI__GCF_001305295.1:WP_054342411.1
Length = 869
Score = 1392 bits (3602), Expect = 0.0
Identities = 691/869 (79%), Positives = 766/869 (88%), Gaps = 5/869 (0%)
Query: 1 MNSANRKPLPGTKLDYFDARAAVEAIQPGAYDKLPYTSRVLAENLVRRCDPATLTDSLLQ 60
MN+ RK LPGTKLDYFD RAA+E IQPG+Y KLPYTSRVLAE LVRRC+P LTDSL Q
Sbjct: 1 MNTEYRKSLPGTKLDYFDTRAAIEDIQPGSYAKLPYTSRVLAEQLVRRCEPEALTDSLKQ 60
Query: 61 LVGRKRDLDFPWFPARVVCHDILGQTALVDLAGLRDAIADQGGDPAKVNPVVPVQLIVDH 120
L+ KR+LDFPW+PARVVCHDILGQTALVDLAGLRDAIA+QGGDP+KVNPVVP QLIVDH
Sbjct: 61 LIEFKRELDFPWYPARVVCHDILGQTALVDLAGLRDAIAEQGGDPSKVNPVVPTQLIVDH 120
Query: 121 SLAVECGGFDPDAFAKNRAIEDRRNEDRFHFIDWTKQAFKNVDVIPPGNGIMHQINLEKM 180
SLAVE GFDPDAF KNRAIEDRRN+DRFHFI+W K AF NVDVIP GNGIMHQINLEKM
Sbjct: 121 SLAVEAAGFDPDAFEKNRAIEDRRNDDRFHFIEWCKTAFDNVDVIPAGNGIMHQINLEKM 180
Query: 181 SPVIHADNGVAYPDTCVGTDSHTPHVDALGVIAIGVGGLEAENVMLGRASWMRLPDIVGV 240
SPVI A +GVAYPDTCVGTDSHTPHVDALGV+AIGVGGLEAE VMLG S MRLPDI+GV
Sbjct: 181 SPVIQARDGVAYPDTCVGTDSHTPHVDALGVLAIGVGGLEAETVMLGLPSMMRLPDIIGV 240
Query: 241 ELTGKRQPGITATDIVLALTEFLRKEKVVGAYLEFRGEGASSLTLGDRATISNMAPEYGA 300
+LTGKRQPGITATDIVLA+TEFLR +KVV AYLEF GEGA +LT+GDRATISNM PE+GA
Sbjct: 241 KLTGKRQPGITATDIVLAITEFLRNQKVVSAYLEFFGEGAKNLTIGDRATISNMTPEFGA 300
Query: 301 TAAMFFIDEQTIDYLRLTGRTDEQLKLVETYARTAGLWADSLKNAEYERVLKFDLSSVVR 360
+A MF+IDEQTI YL+LTGR EQ+ LVE YA+ GLWAD L+N EYERVL+FDLSSVVR
Sbjct: 301 SAGMFYIDEQTIAYLKLTGREPEQVALVEQYAKLTGLWADDLENVEYERVLEFDLSSVVR 360
Query: 361 NMAGPSNPHKRLPTSALAERGIAVD--LDKASAQEAEGLMPDGAVIIAAITSCTNTSNPR 418
NMAGPSNPH+RLPTSAL ERGIA + L A A+E GLMPDGAVIIAAITSCTNTSNPR
Sbjct: 361 NMAGPSNPHRRLPTSALKERGIASEEMLAAAKAEEEAGLMPDGAVIIAAITSCTNTSNPR 420
Query: 419 NVIAAALLARNANARGLARKPWVKSSLAPGSKAVELYLEEANLLPDLEKLGFGIVAFACT 478
NV+AA L+A+ AN GL RKPWVK+S APGSK +LYLEEA LL ++E+LGFGIV +ACT
Sbjct: 421 NVVAAGLVAKKANELGLVRKPWVKTSFAPGSKVAKLYLEEAGLLSEMEQLGFGIVGYACT 480
Query: 479 TCNGMSGALDPKIQQEIIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAG 538
TCNGMSGALDP IQQEIIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAG
Sbjct: 481 TCNGMSGALDPVIQQEIIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAG 540
Query: 539 TIRFDIEKDVLGTDQDGKPVYLKDIWPSDEEIDAIVAKSVKPEQFRKVYEPMFAITAASG 598
TIRFDIEKDVLGTD+DG P+ LKDIWPSDEEID+IVAK+VKPEQF ++Y PMF +
Sbjct: 541 TIRFDIEKDVLGTDKDGNPITLKDIWPSDEEIDSIVAKAVKPEQFSQIYIPMFDLGTVE- 599
Query: 599 ESVSPLYDWRPQSTYIRRPPYWEGALAGERTLKALRPLAVLGDNITTDHLSPSNAIMLNS 658
++VSPLYDWRPQ+TYIRRPPYWEGALAGERT+K +RPLAVLGDNITTDHLSPSNAI +S
Sbjct: 600 KAVSPLYDWRPQTTYIRRPPYWEGALAGERTMKGMRPLAVLGDNITTDHLSPSNAIQASS 659
Query: 659 AAGEYLARMGLPEEDFNSYATHRGDHLTAQRATFANPTLINEMAVVD-GQVKKGSLARIE 717
AAGEY A+MGLPEEDFNSYATHRGDHLTAQRATFANP L+NEM + + G+VK+GSLARIE
Sbjct: 660 AAGEYCAKMGLPEEDFNSYATHRGDHLTAQRATFANPKLLNEMCLDEKGEVKQGSLARIE 719
Query: 718 PEGKVVRMWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEVIVAEGFERIH 777
PEGK RMWEAIETYM+RKQPLII+AGADYGQGSSRDWAAKGVRLAGVE I+AEGFERIH
Sbjct: 720 PEGKESRMWEAIETYMERKQPLIIVAGADYGQGSSRDWAAKGVRLAGVEAIMAEGFERIH 779
Query: 778 RTNLIGMGVLPLEFKPGVNRLTLGLDGTETYDVIGERQPRATLTLVVNRKNGERVEVPVT 837
RTNL+GMGVLPL+FK G R T +DGTET+DV G+ PRA L +++NR NGE V+VP+
Sbjct: 780 RTNLVGMGVLPLQFKEGETRKTYAIDGTETFDVEGDISPRAELNVIINRANGETVKVPMI 839
Query: 838 CRLDSDEEVSIYEAGGVL-HFAQDFLESS 865
CRLD+ EV++Y AGGVL FAQDFLE +
Sbjct: 840 CRLDTAAEVNVYNAGGVLQRFAQDFLEGN 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: 2165
Number of extensions: 84
Number of successful extensions: 5
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_054342411.1 Nant_RS14685 (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.612917.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 1771.1 0.0 0 1771.0 0.0 1.0 1 NCBI__GCF_001305295.1:WP_054342411.1
Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001305295.1:WP_054342411.1
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1771.0 0.0 0 0 1 858 [] 2 866 .. 2 866 .. 0.99
Alignments for each domain:
== domain 1 score: 1771.0 bits; conditional E-value: 0
TIGR02333 1 ntkyrkalpgtdldyfdaraaveaikpgaydklpytsrvlaenlvrrvdpetleaslkqlierkreldfpwyp 73
nt+yrk+lpgt+ldyfd+raa+e+i+pg+y+klpytsrvlae+lvrr++pe l++slkqlie kreldfpwyp
NCBI__GCF_001305295.1:WP_054342411.1 2 NTEYRKSLPGTKLDYFDTRAAIEDIQPGSYAKLPYTSRVLAEQLVRRCEPEALTDSLKQLIEFKRELDFPWYP 74
899********************************************************************** PP
TIGR02333 74 arvvchdilgqtalvdlaglrdaiaekggdpaqvnpvvetqlivdhslaveyggfdpdafeknraiedrrned 146
arvvchdilgqtalvdlaglrdaiae+ggdp++vnpvv+tqlivdhslave +gfdpdafeknraiedrrn+d
NCBI__GCF_001305295.1:WP_054342411.1 75 ARVVCHDILGQTALVDLAGLRDAIAEQGGDPSKVNPVVPTQLIVDHSLAVEAAGFDPDAFEKNRAIEDRRNDD 147
************************************************************************* PP
TIGR02333 147 rfhfinwtkkafknvdvipagngimhqinlekmspvvqvkegvafpdtlvgtdshtphvdalgviaigvggle 219
rfhfi+w+k+af+nvdvipagngimhqinlekmspv+q+++gva+pdt+vgtdshtphvdalgv+aigvggle
NCBI__GCF_001305295.1:WP_054342411.1 148 RFHFIEWCKTAFDNVDVIPAGNGIMHQINLEKMSPVIQARDGVAYPDTCVGTDSHTPHVDALGVLAIGVGGLE 220
************************************************************************* PP
TIGR02333 220 aetvmlgraslmrlpdivgveltgkrqpgitatdivlalteflrkekvvsayleffgegakaltlgdratisn 292
aetvmlg +s+mrlpdi+gv+ltgkrqpgitatdivla+teflr++kvvsayleffgegak lt+gdratisn
NCBI__GCF_001305295.1:WP_054342411.1 221 AETVMLGLPSMMRLPDIIGVKLTGKRQPGITATDIVLAITEFLRNQKVVSAYLEFFGEGAKNLTIGDRATISN 293
************************************************************************* PP
TIGR02333 293 mtpeygataamfaideqtidylkltgreeeqvklvetyakaaglwadslkkavyervlkfdlssvvrnlagps 365
mtpe+ga+a+mf+ideqti ylkltgre+eqv+lve yak +glwad+l++ +yervl+fdlssvvrn+agps
NCBI__GCF_001305295.1:WP_054342411.1 294 MTPEFGASAGMFYIDEQTIAYLKLTGREPEQVALVEQYAKLTGLWADDLENVEYERVLEFDLSSVVRNMAGPS 366
************************************************************************* PP
TIGR02333 366 npharlatsdlaakgiakevee......eaeglmpdgaviiaaitsctntsnprnvvaagllarnanklglkr 432
nph+rl+ts l +gia+e e glmpdgaviiaaitsctntsnprnvvaagl+a++an+lgl r
NCBI__GCF_001305295.1:WP_054342411.1 367 NPHRRLPTSALKERGIASEEMLaaakaeEEAGLMPDGAVIIAAITSCTNTSNPRNVVAAGLVAKKANELGLVR 439
****************975321222222555****************************************** PP
TIGR02333 433 kpwvksslapgskvvklyleeagllkeleklgfgivafacttcngmsgaldpviqqeiidrdlyatavlsgnr 505
kpwvk+s+apgskv+klyleeagll+e+e+lgfgiv++acttcngmsgaldpviqqeiidrdlyatavlsgnr
NCBI__GCF_001305295.1:WP_054342411.1 440 KPWVKTSFAPGSKVAKLYLEEAGLLSEMEQLGFGIVGYACTTCNGMSGALDPVIQQEIIDRDLYATAVLSGNR 512
************************************************************************* PP
TIGR02333 506 nfdgrihpyakqaflaspplvvayaiagtirfdiekdvlgvdadgkeirlkdiwpsdeeidavvaaavkpeqf 578
nfdgrihpyakqaflaspplvvayaiagtirfdiekdvlg+d+dg++i lkdiwpsdeeid++va+avkpeqf
NCBI__GCF_001305295.1:WP_054342411.1 513 NFDGRIHPYAKQAFLASPPLVVAYAIAGTIRFDIEKDVLGTDKDGNPITLKDIWPSDEEIDSIVAKAVKPEQF 585
************************************************************************* PP
TIGR02333 579 rkvyipmfdledaqkkvsplydwrpmstyirrppywegalagertlkgmrplavlgdnittdhlspsnailld 651
++yipmfdl++ +k+vsplydwrp++tyirrppywegalagert+kgmrplavlgdnittdhlspsnai ++
NCBI__GCF_001305295.1:WP_054342411.1 586 SQIYIPMFDLGTVEKAVSPLYDWRPQTTYIRRPPYWEGALAGERTMKGMRPLAVLGDNITTDHLSPSNAIQAS 658
************************************************************************* PP
TIGR02333 652 saageylakmglpeedfnsyathrgdhltaqratfanpklfnemvked.gkvkqgslariepegkvtrmweai 723
saagey akmglpeedfnsyathrgdhltaqratfanpkl nem ++ g+vkqgslariepegk rmweai
NCBI__GCF_001305295.1:WP_054342411.1 659 SAAGEYCAKMGLPEEDFNSYATHRGDHLTAQRATFANPKLLNEMCLDEkGEVKQGSLARIEPEGKESRMWEAI 731
********************************************99988************************ PP
TIGR02333 724 etymnrkqpliiiagadygqgssrdwaakgvrlagveaivaegferihrtnlvgmgvlplefkpgtnrktlal 796
etym+rkqplii+agadygqgssrdwaakgvrlagveai+aegferihrtnlvgmgvlpl+fk g+ rkt+a+
NCBI__GCF_001305295.1:WP_054342411.1 732 ETYMERKQPLIIVAGADYGQGSSRDWAAKGVRLAGVEAIMAEGFERIHRTNLVGMGVLPLQFKEGETRKTYAI 804
************************************************************************* PP
TIGR02333 797 dgtevydvvgeitpradltlvvtrkngeklevpvtcrldtaeevsvyeaggvlqrfaqdfle 858
dgte++dv g+i+pra+l ++++r+nge+++vp+ crldta ev+vy+aggvlqrfaqdfle
NCBI__GCF_001305295.1:WP_054342411.1 805 DGTETFDVEGDISPRAELNVIINRANGETVKVPMICRLDTAAEVNVYNAGGVLQRFAQDFLE 866
************************************************************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: 25.78
//
[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