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_011280385.1 PSYC_RS05785 Fe/S-dependent 2-methylisocitrate dehydratase AcnD
Query= SwissProt::Q937N8
(869 letters)
>NCBI__GCF_000012305.1:WP_011280385.1
Length = 885
Score = 1246 bits (3225), Expect = 0.0
Identities = 618/873 (70%), Positives = 726/873 (83%), Gaps = 8/873 (0%)
Query: 1 MNSANRKPLPGTKLDYFDARAAVEAIQPGAYDKLPYTSRVLAENLVRRCDPATLTDSLLQ 60
MN +KPLPGT L YFD R A+E I+ GAYDKLP+ S+VL ENLVRRC P LT +L Q
Sbjct: 9 MNEPFKKPLPGTDLYYFDTREAIENIEAGAYDKLPFCSKVLCENLVRRCPPEDLTAALEQ 68
Query: 61 LVGRKRDLDFPWFPARVVCHDILGQTALVDLAGLRDAIADQGGDPAKVNPVVPVQLIVDH 120
+ K+DLDFPW+PARVVCHDILGQTA VDLAGLRDAIA+QGGDP+KVNP+VP QLIVDH
Sbjct: 69 HIYGKQDLDFPWYPARVVCHDILGQTAFVDLAGLRDAIAEQGGDPSKVNPIVPTQLIVDH 128
Query: 121 SLAVECGGFDPDAFAKNRAIEDRRNEDRFHFIDWTKQAFKNVDVIPPGNGIMHQINLEKM 180
SLAVE GF+ +AF KNRAIE+RRN+DRFHFI+W + AF NV+V+PPGNGIMHQINLEKM
Sbjct: 129 SLAVEHAGFEENAFEKNRAIEERRNDDRFHFINWCQYAFDNVNVVPPGNGIMHQINLEKM 188
Query: 181 SPVIH-----ADNGVAYPDTCVGTDSHTPHVDALGVIAIGVGGLEAENVMLGRASWMRLP 235
SPV+ A VA+ DT VGTDSHTP VDALGVI+IGVGGLEAE+VMLG S+MRLP
Sbjct: 189 SPVVQVVKNKAGEEVAFADTLVGTDSHTPMVDALGVISIGVGGLEAESVMLGNPSYMRLP 248
Query: 236 DIVGVELTGKRQPGITATDIVLALTEFLRKEKVVGAYLEFRGEGASSLTLGDRATISNMA 295
D VGV+LTGK Q GIT TD+VLA+TEFLR VV Y+EF GEGA L++GDRA+ISNM
Sbjct: 249 DYVGVKLTGKLQKGITGTDLVLAMTEFLRNAGVVSTYIEFFGEGARQLSVGDRASISNMT 308
Query: 296 PEYGATAAMFFIDEQTIDYLRLTGRTDEQLKLVETYARTAGLWADSLKNAEYERVLKFDL 355
PEYGATAAMF+IDEQTIDYLRLTGR++ Q+KLVE YA+ GLWAD ++NA Y+RVL+FDL
Sbjct: 309 PEYGATAAMFYIDEQTIDYLRLTGRSEAQIKLVEQYAKQTGLWADGMENAVYDRVLEFDL 368
Query: 356 SSVVRNMAGPSNPHKRLPTSALAERGIAVDLDKASAQEAEGLMPDGAVIIAAITSCTNTS 415
S+VVRNMAGPS PH R+ T+ L +GIA + + +GLMPDGAVIIAAITSCTNTS
Sbjct: 369 SAVVRNMAGPSRPHARVSTTDLVAKGIAHAPEDKLPEPKDGLMPDGAVIIAAITSCTNTS 428
Query: 416 NPRNVIAAALLARNANARGLARKPWVKSSLAPGSKAVELYLEEANLLPDLEKLGFGIVAF 475
NPRN++AA L+ARNANA+GL RKPWVKSSLAPGSK V++YLEEA L+P+L+++GF +V F
Sbjct: 429 NPRNMVAAGLVARNANAKGLLRKPWVKSSLAPGSKTVKMYLEEAGLMPELQEIGFDVVGF 488
Query: 476 ACTTCNGMSGALDPKIQQEIIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYA 535
ACTTCNGMSGALDP I++EIID DL+ TAVLSGNRNFDGRIHPYAKQAFLASPPLV+AYA
Sbjct: 489 ACTTCNGMSGALDPDIEKEIIDNDLFTTAVLSGNRNFDGRIHPYAKQAFLASPPLVIAYA 548
Query: 536 IAGTIRFDIEKDVLGTDQDGKPVYLKDIWPSDEEIDAIVAKSVKPEQFRKVYEPMF-AIT 594
IAG IRFDIEKD LG DQ+G VYLKDIW D+E+DAIVAK+VKPEQF VY PMF
Sbjct: 549 IAGNIRFDIEKDSLGKDQNGNDVYLKDIWFDDDEVDAIVAKAVKPEQFNAVYIPMFDEAK 608
Query: 595 AASGESVSPLYDWRPQSTYIRRPPYWEGALAGERTLKALRPLAVLGDNITTDHLSPSNAI 654
+G+++SPLY+WR Q+TYIRRPPYWEG +A L +RPLAVLGDNITTDHLSPSNAI
Sbjct: 609 KDTGKALSPLYNWRDQTTYIRRPPYWEGKMAAMNKLTGMRPLAVLGDNITTDHLSPSNAI 668
Query: 655 MLNSAAGEYLARMGLPEEDFNSYATHRGDHLTAQRATFANPTLINEMAVVD-GQVKKGSL 713
+ +SAAGEYL MGLP ED+NSYATHRGDHLTAQRATFANP L+NEM + G V +GSL
Sbjct: 669 LGDSAAGEYLDTMGLPSEDYNSYATHRGDHLTAQRATFANPKLLNEMVRDEKGDVIQGSL 728
Query: 714 ARIEPEGKVVRMWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEVIVAEGF 773
AR+EPEG+V+RMWEAIETYM+R+QPLIIIAG YGQGSSRDWAAKGVRLAGVEV+VAE F
Sbjct: 729 ARVEPEGQVMRMWEAIETYMNREQPLIIIAGDGYGQGSSRDWAAKGVRLAGVEVVVAEDF 788
Query: 774 ERIHRTNLIGMGVLPLEFKPGVNRLTLGLDGTETYDVIGERQPRATLTLVVNRKNGERVE 833
ERIHR NL+GMG LPL+F+ GV R TL +DGTE +DV GE + LV+NR +G ++E
Sbjct: 789 ERIHRQNLVGMGALPLQFEKGVTRNTLNIDGTEVFDVTGEVSAGGMMALVINRADGSKLE 848
Query: 834 VPVTCRLDSDEEVSIYEAGGVL-HFAQDFLESS 865
VP+ CRLD+ +EV +Y AGG+L FA++F++ +
Sbjct: 849 VPIICRLDTADEVKMYNAGGMLQRFAKEFIDGT 881
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: 2117
Number of extensions: 74
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: 885
Length adjustment: 42
Effective length of query: 827
Effective length of database: 843
Effective search space: 697161
Effective search space used: 697161
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_011280385.1 PSYC_RS05785 (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.3826808.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 1592.5 0.1 0 1592.3 0.1 1.0 1 NCBI__GCF_000012305.1:WP_011280385.1
Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000012305.1:WP_011280385.1
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1592.3 0.1 0 0 1 857 [. 10 878 .. 10 879 .. 0.98
Alignments for each domain:
== domain 1 score: 1592.3 bits; conditional E-value: 0
TIGR02333 1 ntkyrkalpgtdldyfdaraaveaikpgaydklpytsrvlaenlvrrvdpetleaslkqlierkreldfpwyp 73
n+ ++k+lpgtdl yfd+r+a+e+i+ gaydklp+ s+vl+enlvrr++pe l+a+l+q i +k++ldfpwyp
NCBI__GCF_000012305.1:WP_011280385.1 10 NEPFKKPLPGTDLYYFDTREAIENIEAGAYDKLPFCSKVLCENLVRRCPPEDLTAALEQHIYGKQDLDFPWYP 82
56799******************************************************************** PP
TIGR02333 74 arvvchdilgqtalvdlaglrdaiaekggdpaqvnpvvetqlivdhslaveyggfdpdafeknraiedrrned 146
arvvchdilgqta+vdlaglrdaiae+ggdp++vnp+v+tqlivdhslave +gf+++afeknraie+rrn+d
NCBI__GCF_000012305.1:WP_011280385.1 83 ARVVCHDILGQTAFVDLAGLRDAIAEQGGDPSKVNPIVPTQLIVDHSLAVEHAGFEENAFEKNRAIEERRNDD 155
************************************************************************* PP
TIGR02333 147 rfhfinwtkkafknvdvipagngimhqinlekmspvvqv...k..egvafpdtlvgtdshtphvdalgviaig 214
rfhfinw++ af+nv+v+p+gngimhqinlekmspvvqv k e vaf dtlvgtdshtp vdalgvi+ig
NCBI__GCF_000012305.1:WP_011280385.1 156 RFHFINWCQYAFDNVNVVPPGNGIMHQINLEKMSPVVQVvknKagEEVAFADTLVGTDSHTPMVDALGVISIG 228
************************************997322222469************************* PP
TIGR02333 215 vggleaetvmlgraslmrlpdivgveltgkrqpgitatdivlalteflrkekvvsayleffgegakaltlgdr 287
vggleae+vmlg +s+mrlpd vgv+ltgk q git td+vla+teflr+ vvs+y+effgega+ l++gdr
NCBI__GCF_000012305.1:WP_011280385.1 229 VGGLEAESVMLGNPSYMRLPDYVGVKLTGKLQKGITGTDLVLAMTEFLRNAGVVSTYIEFFGEGARQLSVGDR 301
************************************************************************* PP
TIGR02333 288 atisnmtpeygataamfaideqtidylkltgreeeqvklvetyakaaglwadslkkavyervlkfdlssvvrn 360
a+isnmtpeygataamf+ideqtidyl+ltgr e+q+klve yak +glwad +++avy+rvl+fdls+vvrn
NCBI__GCF_000012305.1:WP_011280385.1 302 ASISNMTPEYGATAAMFYIDEQTIDYLRLTGRSEAQIKLVEQYAKQTGLWADGMENAVYDRVLEFDLSAVVRN 374
************************************************************************* PP
TIGR02333 361 lagpsnpharlatsdlaakgiakevee....eaeglmpdgaviiaaitsctntsnprnvvaagllarnanklg 429
+agps phar++t+dl akgia+ e+ +glmpdgaviiaaitsctntsnprn+vaagl+arnan++g
NCBI__GCF_000012305.1:WP_011280385.1 375 MAGPSRPHARVSTTDLVAKGIAHAPEDklpePKDGLMPDGAVIIAAITSCTNTSNPRNMVAAGLVARNANAKG 447
**********************988876665789*************************************** PP
TIGR02333 430 lkrkpwvksslapgskvvklyleeagllkeleklgfgivafacttcngmsgaldpviqqeiidrdlyatavls 502
l rkpwvksslapgsk+vk+yleeagl++el+++gf +v+facttcngmsgaldp i++eiid dl++tavls
NCBI__GCF_000012305.1:WP_011280385.1 448 LLRKPWVKSSLAPGSKTVKMYLEEAGLMPELQEIGFDVVGFACTTCNGMSGALDPDIEKEIIDNDLFTTAVLS 520
************************************************************************* PP
TIGR02333 503 gnrnfdgrihpyakqaflaspplvvayaiagtirfdiekdvlgvdadgkeirlkdiwpsdeeidavvaaavkp 575
gnrnfdgrihpyakqaflaspplv+ayaiag irfdiekd lg+d++g++++lkdiw d+e+da+va+avkp
NCBI__GCF_000012305.1:WP_011280385.1 521 GNRNFDGRIHPYAKQAFLASPPLVIAYAIAGNIRFDIEKDSLGKDQNGNDVYLKDIWFDDDEVDAIVAKAVKP 593
************************************************************************* PP
TIGR02333 576 eqfrkvyipmfdle..daqkkvsplydwrpmstyirrppywegalagertlkgmrplavlgdnittdhlspsn 646
eqf+ vyipmfd d++k+ sply+wr ++tyirrppyweg +a+ l gmrplavlgdnittdhlspsn
NCBI__GCF_000012305.1:WP_011280385.1 594 EQFNAVYIPMFDEAkkDTGKALSPLYNWRDQTTYIRRPPYWEGKMAAMNKLTGMRPLAVLGDNITTDHLSPSN 666
***********9765699******************************************************* PP
TIGR02333 647 ailldsaageylakmglpeedfnsyathrgdhltaqratfanpklfnemvked.gkvkqgslariepegkvtr 718
ail dsaageyl mglp ed+nsyathrgdhltaqratfanpkl nemv+++ g+v qgslar+epeg+v+r
NCBI__GCF_000012305.1:WP_011280385.1 667 AILGDSAAGEYLDTMGLPSEDYNSYATHRGDHLTAQRATFANPKLLNEMVRDEkGDVIQGSLARVEPEGQVMR 739
***************************************************999******************* PP
TIGR02333 719 mweaietymnrkqpliiiagadygqgssrdwaakgvrlagveaivaegferihrtnlvgmgvlplefkpgtnr 791
mweaietymnr qpliiiag ygqgssrdwaakgvrlagve +vae ferihr nlvgmg lpl+f g+ r
NCBI__GCF_000012305.1:WP_011280385.1 740 MWEAIETYMNREQPLIIIAGDGYGQGSSRDWAAKGVRLAGVEVVVAEDFERIHRQNLVGMGALPLQFEKGVTR 812
************************************************************************* PP
TIGR02333 792 ktlaldgtevydvvgeitpradltlvvtrkngeklevpvtcrldtaeevsvyeaggvlqrfaqdfl 857
+tl++dgtev+dv ge++ + ++lv++r++g klevp+ crldta+ev++y+agg+lqrfa++f+
NCBI__GCF_000012305.1:WP_011280385.1 813 NTLNIDGTEVFDVTGEVSAGGMMALVINRADGSKLEVPIICRLDTADEVKMYNAGGMLQRFAKEFI 878
****************************************************************98 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (858 nodes)
Target sequences: 1 (885 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: 33.34
//
[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