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 5209348 Shew_1822 aconitate hydratase (RefSeq)
Query= SwissProt::Q937N8
(869 letters)
>FitnessBrowser__PV4:5209348
Length = 862
Score = 1422 bits (3680), Expect = 0.0
Identities = 705/866 (81%), Positives = 776/866 (89%), Gaps = 6/866 (0%)
Query: 1 MNSANRKPLPGTKLDYFDARAAVEAIQPGAYDKLPYTSRVLAENLVRRCDPATLTDSLLQ 60
MNS +RKPLPG+ LDYFD RAAVEA+ GAYDKLPYT++VLAENLVRRC+P L D+L Q
Sbjct: 1 MNSLHRKPLPGSALDYFDTRAAVEALSAGAYDKLPYTAKVLAENLVRRCEPELLNDALSQ 60
Query: 61 LVGRKRDLDFPWFPARVVCHDILGQTALVDLAGLRDAIADQGGDPAKVNPVVPVQLIVDH 120
L+ RKRDLDFPW+PARVVCHDILGQTALVDLAGLRDAIA++GGDP+KVNPVVP QLIVDH
Sbjct: 61 LIDRKRDLDFPWYPARVVCHDILGQTALVDLAGLRDAIAEKGGDPSKVNPVVPTQLIVDH 120
Query: 121 SLAVECGGFDPDAFAKNRAIEDRRNEDRFHFIDWTKQAFKNVDVIPPGNGIMHQINLEKM 180
SLAVE GF+ DAF KNRAIEDRRNEDRFHFI+WTK AFKNVDVI PGNGIMHQINLEKM
Sbjct: 121 SLAVEHAGFEKDAFEKNRAIEDRRNEDRFHFINWTKTAFKNVDVIQPGNGIMHQINLEKM 180
Query: 181 SPVIHADNGVAYPDTCVGTDSHTPHVDALGVIAIGVGGLEAENVMLGRASWMRLPDIVGV 240
SPVI A +GVA+PDT VGTDSHTPHVDALGVIAIGVGGLEAENVMLGR S+MRLPDIVGV
Sbjct: 181 SPVIQARDGVAFPDTLVGTDSHTPHVDALGVIAIGVGGLEAENVMLGRPSYMRLPDIVGV 240
Query: 241 ELTGKRQPGITATDIVLALTEFLRKEKVVGAYLEFRGEGASSLTLGDRATISNMAPEYGA 300
ELTGKRQ GITATDIVLALTEFLR+EKVV AYLEF GEGA+ LTLGDRATISNM PE+GA
Sbjct: 241 ELTGKRQSGITATDIVLALTEFLRQEKVVSAYLEFFGEGAADLTLGDRATISNMTPEFGA 300
Query: 301 TAAMFFIDEQTIDYLRLTGRTDEQLKLVETYARTAGLWADSLKNAEYERVLKFDLSSVVR 360
+A MF+ID+QTIDYL +TGR EQ+KLVE YA+T GLWADSLK+AEYERVL FDLSSVVR
Sbjct: 301 SAGMFYIDQQTIDYLTITGRDSEQVKLVENYAKTTGLWADSLKDAEYERVLTFDLSSVVR 360
Query: 361 NMAGPSNPHKRLPTSALAERGIAVDLDKASAQEAEGLMPDGAVIIAAITSCTNTSNPRNV 420
N+AGPSNPH+R+ TS LA +GIA ++ + LMPDGAVIIAAITSCTNTSNPRNV
Sbjct: 361 NIAGPSNPHRRVATSELASQGIA-----GVVEQDDKLMPDGAVIIAAITSCTNTSNPRNV 415
Query: 421 IAAALLARNANARGLARKPWVKSSLAPGSKAVELYLEEANLLPDLEKLGFGIVAFACTTC 480
IAA LLA+ AN GL RKPWVK+S APGSK ELYL++A LLP+LE+LGFGIV FACTTC
Sbjct: 416 IAAGLLAKKANELGLVRKPWVKTSFAPGSKVAELYLKDAGLLPELEQLGFGIVGFACTTC 475
Query: 481 NGMSGALDPKIQQEIIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTI 540
NGMSGALDP IQQE+IDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTI
Sbjct: 476 NGMSGALDPVIQQEVIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTI 535
Query: 541 RFDIEKDVLGTDQDGKPVYLKDIWPSDEEIDAIVAKSVKPEQFRKVYEPMFAITAASGES 600
RFDIEKD+LG D G+P+ LKDIWPSDEEIDAIV SVKP+QFR +Y PMF + GE
Sbjct: 536 RFDIEKDILGHDDKGEPIRLKDIWPSDEEIDAIVKASVKPQQFRDIYTPMFDLAVDYGED 595
Query: 601 VSPLYDWRPQSTYIRRPPYWEGALAGERTLKALRPLAVLGDNITTDHLSPSNAIMLNSAA 660
V+PLYDWRPQSTYIRRPPYWEGALAGERTLK +RPLAVLGDNITTDHLSPSNAI+ +SAA
Sbjct: 596 VNPLYDWRPQSTYIRRPPYWEGALAGERTLKGMRPLAVLGDNITTDHLSPSNAILASSAA 655
Query: 661 GEYLARMGLPEEDFNSYATHRGDHLTAQRATFANPTLINEMAVVDGQVKKGSLARIEPEG 720
GEYLA+MGLPE DFNSYATHRGDHLTAQRATFANP LINEMA+VDG+VK+GSL R+EPEG
Sbjct: 656 GEYLAKMGLPEVDFNSYATHRGDHLTAQRATFANPKLINEMALVDGEVKQGSLTRLEPEG 715
Query: 721 KVVRMWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEVIVAEGFERIHRTN 780
+V+RMWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVE IVAEGFERIHRTN
Sbjct: 716 EVMRMWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEAIVAEGFERIHRTN 775
Query: 781 LIGMGVLPLEFKPGVNRLTLGLDGTETYDVIGERQPRATLTLVVNRKNGERVEVPVTCRL 840
L+GMGVLPLEFK G NR T G+DG+ET+DVIGE PRA LT+V+ R+NGERVEVPV CRL
Sbjct: 776 LVGMGVLPLEFKAGENRHTYGIDGSETFDVIGEPTPRADLTVVITRQNGERVEVPVICRL 835
Query: 841 DSDEEVSIYEAGGVL-HFAQDFLESS 865
D+ +EV +Y+AGGVL FAQDFLE++
Sbjct: 836 DTADEVLVYQAGGVLQRFAQDFLEAN 861
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: 2181
Number of extensions: 86
Number of successful extensions: 3
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: 862
Length adjustment: 42
Effective length of query: 827
Effective length of database: 820
Effective search space: 678140
Effective search space used: 678140
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 5209348 Shew_1822 (aconitate hydratase (RefSeq))
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.10721.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 1801.5 0.0 0 1801.3 0.0 1.0 1 lcl|FitnessBrowser__PV4:5209348 Shew_1822 aconitate hydratase (R
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PV4:5209348 Shew_1822 aconitate hydratase (RefSeq)
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1801.3 0.0 0 0 1 858 [] 2 859 .. 2 859 .. 1.00
Alignments for each domain:
== domain 1 score: 1801.3 bits; conditional E-value: 0
TIGR02333 1 ntkyrkalpgtdldyfdaraaveaikpgaydklpytsrvlaenlvrrvdpetleaslkqlierkreldfpwyparvvc 78
n+ +rk+lpg++ldyfd+raavea+ gaydklpyt++vlaenlvrr++pe l+++l+qli+rkr+ldfpwyparvvc
lcl|FitnessBrowser__PV4:5209348 2 NSLHRKPLPGSALDYFDTRAAVEALSAGAYDKLPYTAKVLAENLVRRCEPELLNDALSQLIDRKRDLDFPWYPARVVC 79
7889************************************************************************** PP
TIGR02333 79 hdilgqtalvdlaglrdaiaekggdpaqvnpvvetqlivdhslaveyggfdpdafeknraiedrrnedrfhfinwtkk 156
hdilgqtalvdlaglrdaiaekggdp++vnpvv+tqlivdhslave +gf++dafeknraiedrrnedrfhfinwtk+
lcl|FitnessBrowser__PV4:5209348 80 HDILGQTALVDLAGLRDAIAEKGGDPSKVNPVVPTQLIVDHSLAVEHAGFEKDAFEKNRAIEDRRNEDRFHFINWTKT 157
****************************************************************************** PP
TIGR02333 157 afknvdvipagngimhqinlekmspvvqvkegvafpdtlvgtdshtphvdalgviaigvggleaetvmlgraslmrlp 234
afknvdvi++gngimhqinlekmspv+q+++gvafpdtlvgtdshtphvdalgviaigvggleae+vmlgr+s+mrlp
lcl|FitnessBrowser__PV4:5209348 158 AFKNVDVIQPGNGIMHQINLEKMSPVIQARDGVAFPDTLVGTDSHTPHVDALGVIAIGVGGLEAENVMLGRPSYMRLP 235
****************************************************************************** PP
TIGR02333 235 divgveltgkrqpgitatdivlalteflrkekvvsayleffgegakaltlgdratisnmtpeygataamfaideqtid 312
divgveltgkrq+gitatdivlalteflr+ekvvsayleffgega ltlgdratisnmtpe+ga+a+mf+id+qtid
lcl|FitnessBrowser__PV4:5209348 236 DIVGVELTGKRQSGITATDIVLALTEFLRQEKVVSAYLEFFGEGAADLTLGDRATISNMTPEFGASAGMFYIDQQTID 313
****************************************************************************** PP
TIGR02333 313 ylkltgreeeqvklvetyakaaglwadslkkavyervlkfdlssvvrnlagpsnpharlatsdlaakgiakeveeeae 390
yl++tgr++eqvklve yak++glwadslk+a+yervl+fdlssvvrn+agpsnph+r+ats+la++gia+ ve++
lcl|FitnessBrowser__PV4:5209348 314 YLTITGRDSEQVKLVENYAKTTGLWADSLKDAEYERVLTFDLSSVVRNIAGPSNPHRRVATSELASQGIAGVVEQDD- 390
***********************************************************************999876. PP
TIGR02333 391 glmpdgaviiaaitsctntsnprnvvaagllarnanklglkrkpwvksslapgskvvklyleeagllkeleklgfgiv 468
lmpdgaviiaaitsctntsnprnv+aaglla++an+lgl rkpwvk+s+apgskv++lyl++agll+ele+lgfgiv
lcl|FitnessBrowser__PV4:5209348 391 KLMPDGAVIIAAITSCTNTSNPRNVIAAGLLAKKANELGLVRKPWVKTSFAPGSKVAELYLKDAGLLPELEQLGFGIV 468
9***************************************************************************** PP
TIGR02333 469 afacttcngmsgaldpviqqeiidrdlyatavlsgnrnfdgrihpyakqaflaspplvvayaiagtirfdiekdvlgv 546
+facttcngmsgaldpviqqe+idrdlyatavlsgnrnfdgrihpyakqaflaspplvvayaiagtirfdiekd+lg+
lcl|FitnessBrowser__PV4:5209348 469 GFACTTCNGMSGALDPVIQQEVIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTIRFDIEKDILGH 546
****************************************************************************** PP
TIGR02333 547 dadgkeirlkdiwpsdeeidavvaaavkpeqfrkvyipmfdle.daqkkvsplydwrpmstyirrppywegalagert 623
d +g +irlkdiwpsdeeida+v+a+vkp+qfr++y pmfdl d+++ v plydwrp+styirrppywegalagert
lcl|FitnessBrowser__PV4:5209348 547 DDKGEPIRLKDIWPSDEEIDAIVKASVKPQQFRDIYTPMFDLAvDYGEDVNPLYDWRPQSTYIRRPPYWEGALAGERT 624
*******************************************9********************************** PP
TIGR02333 624 lkgmrplavlgdnittdhlspsnailldsaageylakmglpeedfnsyathrgdhltaqratfanpklfnemvkedgk 701
lkgmrplavlgdnittdhlspsnail++saageylakmglpe dfnsyathrgdhltaqratfanpkl+nem+ +dg+
lcl|FitnessBrowser__PV4:5209348 625 LKGMRPLAVLGDNITTDHLSPSNAILASSAAGEYLAKMGLPEVDFNSYATHRGDHLTAQRATFANPKLINEMALVDGE 702
****************************************************************************** PP
TIGR02333 702 vkqgslariepegkvtrmweaietymnrkqpliiiagadygqgssrdwaakgvrlagveaivaegferihrtnlvgmg 779
vkqgsl+r+epeg+v+rmweaietym+rkqpliiiagadygqgssrdwaakgvrlagveaivaegferihrtnlvgmg
lcl|FitnessBrowser__PV4:5209348 703 VKQGSLTRLEPEGEVMRMWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEAIVAEGFERIHRTNLVGMG 780
****************************************************************************** PP
TIGR02333 780 vlplefkpgtnrktlaldgtevydvvgeitpradltlvvtrkngeklevpvtcrldtaeevsvyeaggvlqrfaqdfl 857
vlplefk+g+nr+t+++dg+e++dv+ge tpradlt+v+tr+nge++evpv crldta+ev vy+aggvlqrfaqdfl
lcl|FitnessBrowser__PV4:5209348 781 VLPLEFKAGENRHTYGIDGSETFDVIGEPTPRADLTVVITRQNGERVEVPVICRLDTADEVLVYQAGGVLQRFAQDFL 858
*****************************************************************************9 PP
TIGR02333 858 e 858
e
lcl|FitnessBrowser__PV4:5209348 859 E 859
7 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (858 nodes)
Target sequences: 1 (862 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: 0.06u 0.03s 00:00:00.09 Elapsed: 00:00:00.07
# Mc/sec: 9.39
//
[ok]
This GapMind analysis is from Sep 17 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