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 GFF1973 HP15_1930 aconitate hydratase 1
Query= SwissProt::Q937N8
(869 letters)
>FitnessBrowser__Marino:GFF1973
Length = 865
Score = 1387 bits (3590), Expect = 0.0
Identities = 692/869 (79%), Positives = 757/869 (87%), Gaps = 7/869 (0%)
Query: 1 MNSANRKPLPGTKLDYFDARAAVEAIQPGAYDKLPYTSRVLAENLVRRCDPATLTDSLLQ 60
MN+ RK LPGT LDYFD R AVE IQ GAYDKLPYTS++LAE LVRRCDP LTDSL Q
Sbjct: 1 MNTEYRKSLPGTDLDYFDTRQAVEDIQAGAYDKLPYTSKILAEQLVRRCDPEVLTDSLKQ 60
Query: 61 LVGRKRDLDFPWFPARVVCHDILGQTALVDLAGLRDAIADQGGDPAKVNPVVPVQLIVDH 120
L+ RKRDLDFPW+PARVVCHDILGQTALVDLAGLRDAIA++GGDPAKVNPVVP QLIVDH
Sbjct: 61 LIERKRDLDFPWYPARVVCHDILGQTALVDLAGLRDAIAEKGGDPAKVNPVVPTQLIVDH 120
Query: 121 SLAVECGGFDPDAFAKNRAIEDRRNEDRFHFIDWTKQAFKNVDVIPPGNGIMHQINLEKM 180
SLAVE GF+ DAF KNR IEDRRN+DRFHFI+WTK AFKNVDVIPPGNGIMHQINLEKM
Sbjct: 121 SLAVEHAGFEKDAFEKNREIEDRRNDDRFHFINWTKTAFKNVDVIPPGNGIMHQINLEKM 180
Query: 181 SPVIHADNGVAYPDTCVGTDSHTPHVDALGVIAIGVGGLEAENVMLGRASWMRLPDIVGV 240
SPV+ +GVA+PDTCVGTDSHTP VDALGVI++GVGGLEAE+VMLGRAS MRLPDIVGV
Sbjct: 181 SPVVQNRDGVAFPDTCVGTDSHTPMVDALGVISVGVGGLEAESVMLGRASMMRLPDIVGV 240
Query: 241 ELTGKRQPGITATDIVLALTEFLRKEKVVGAYLEFRGEGASSLTLGDRATISNMAPEYGA 300
ELTGK QPGIT+TD+VLA+TEFLRKEKVVGAYLEF GEGA SL++GDRATISNM PEYGA
Sbjct: 241 ELTGKLQPGITSTDMVLAITEFLRKEKVVGAYLEFYGEGADSLSVGDRATISNMTPEYGA 300
Query: 301 TAAMFFIDEQTIDYLRLTGRTDEQLKLVETYARTAGLWADSLKNAEYERVLKFDLSSVVR 360
TAAMF+ID QTIDYL+LTGR D+Q+ LVE +A+ GLWADS+KNAEYERVLKFDLS V R
Sbjct: 301 TAAMFYIDGQTIDYLKLTGREDDQVALVEKFAKETGLWADSMKNAEYERVLKFDLSKVTR 360
Query: 361 NMAGPSNPHKRLPTSALAERGIAVDLDKASAQEAEGLMPDGAVIIAAITSCTNTSNPRNV 420
+AGPSNPH LPTS LA RGIA ++ EG MPDGA IIAAITSCTNTSNPRN+
Sbjct: 361 TLAGPSNPHAHLPTSELAARGIA-----GEWEQEEGKMPDGACIIAAITSCTNTSNPRNM 415
Query: 421 IAAALLARNANARGLARKPWVKSSLAPGSKAVELYLEEANLLPDLEKLGFGIVAFACTTC 480
+AA L+ARNAN GL RKPWVK+SLAPGSK V++YLEEA LLP+LE+LGFG+VAFACTTC
Sbjct: 416 VAAGLIARNANKLGLTRKPWVKTSLAPGSKTVKMYLEEAKLLPELEQLGFGVVAFACTTC 475
Query: 481 NGMSGALDPKIQQEIIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTI 540
NGMSGALDPKI QEI+DRDL++TAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTI
Sbjct: 476 NGMSGALDPKIAQEIMDRDLFSTAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTI 535
Query: 541 RFDIEKDVLGTDQDGKPVYLKDIWPSDEEIDAIVAKSVKPEQFRKVYEPMFAITAASGES 600
RFDIEKD LG DQDG PV LKDIWP D EIDAIV SVKPEQFR Y PMF IT + +
Sbjct: 536 RFDIEKDALGYDQDGNPVTLKDIWPDDAEIDAIVKSSVKPEQFRSTYIPMFDITRDAQAN 595
Query: 601 VSPLYDWRPQSTYIRRPPYWEGALAGERTLKALRPLAVLGDNITTDHLSPSNAIMLNSAA 660
+PLY WRPQSTYIRRPPYWEG + GE+TLK +RPLAVL DNITTDHLSPSNAIM+NSAA
Sbjct: 596 TNPLYKWRPQSTYIRRPPYWEGGMVGEKTLKGMRPLAVLPDNITTDHLSPSNAIMMNSAA 655
Query: 661 GEYLARMGLPEEDFNSYATHRGDHLTAQRATFANPTLINEMA-VVDGQVKKGSLARIEPE 719
GEYL +MG+PEEDFNSYATHRGDHLTAQRATFANP L NEM +G VK+GSLARIEPE
Sbjct: 656 GEYLHKMGVPEEDFNSYATHRGDHLTAQRATFANPKLFNEMVRDENGNVKQGSLARIEPE 715
Query: 720 GKVVRMWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEVIVAEGFERIHRT 779
GKVVRMWEAIETYM+RKQPLIIIAGADYGQGSSRDWAAKGV LAGVE IVAEGFERIHRT
Sbjct: 716 GKVVRMWEAIETYMERKQPLIIIAGADYGQGSSRDWAAKGVALAGVEAIVAEGFERIHRT 775
Query: 780 NLIGMGVLPLEFKPGVNRLTLGLDGTETYDVIGERQPRATLTLVVNRKNGERVEVPVTCR 839
NLIGMGV+PL+F+ G R TLG+DGTETYDV G PRA LTLV++RKNG +PV CR
Sbjct: 776 NLIGMGVMPLQFEEGTTRKTLGIDGTETYDVEGTPAPRAELTLVIHRKNGSTERIPVVCR 835
Query: 840 LDSDEEVSIYEAGGVL-HFAQDFLESSRA 867
LD+ EEVSIY AGGVL FA+DFL+S A
Sbjct: 836 LDTAEEVSIYSAGGVLQRFAEDFLQSEGA 864
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: 2137
Number of extensions: 83
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: 865
Length adjustment: 42
Effective length of query: 827
Effective length of database: 823
Effective search space: 680621
Effective search space used: 680621
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 GFF1973 HP15_1930 (aconitate hydratase 1)
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.21788.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 1755.9 0.0 0 1755.7 0.0 1.0 1 lcl|FitnessBrowser__Marino:GFF1973 HP15_1930 aconitate hydratase 1
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Marino:GFF1973 HP15_1930 aconitate hydratase 1
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1755.7 0.0 0 0 1 858 [] 2 860 .. 2 860 .. 1.00
Alignments for each domain:
== domain 1 score: 1755.7 bits; conditional E-value: 0
TIGR02333 1 ntkyrkalpgtdldyfdaraaveaikpgaydklpytsrvlaenlvrrvdpetleaslkqlierkreldfpwypar 75
nt+yrk+lpgtdldyfd+r+ave+i+ gaydklpyts++lae+lvrr+dpe l++slkqlierkr+ldfpwypar
lcl|FitnessBrowser__Marino:GFF1973 2 NTEYRKSLPGTDLDYFDTRQAVEDIQAGAYDKLPYTSKILAEQLVRRCDPEVLTDSLKQLIERKRDLDFPWYPAR 76
899************************************************************************ PP
TIGR02333 76 vvchdilgqtalvdlaglrdaiaekggdpaqvnpvvetqlivdhslaveyggfdpdafeknraiedrrnedrfhf 150
vvchdilgqtalvdlaglrdaiaekggdpa+vnpvv+tqlivdhslave +gf++dafeknr+iedrrn+drfhf
lcl|FitnessBrowser__Marino:GFF1973 77 VVCHDILGQTALVDLAGLRDAIAEKGGDPAKVNPVVPTQLIVDHSLAVEHAGFEKDAFEKNREIEDRRNDDRFHF 151
*************************************************************************** PP
TIGR02333 151 inwtkkafknvdvipagngimhqinlekmspvvqvkegvafpdtlvgtdshtphvdalgviaigvggleaetvml 225
inwtk+afknvdvip+gngimhqinlekmspvvq ++gvafpdt+vgtdshtp vdalgvi++gvggleae+vml
lcl|FitnessBrowser__Marino:GFF1973 152 INWTKTAFKNVDVIPPGNGIMHQINLEKMSPVVQNRDGVAFPDTCVGTDSHTPMVDALGVISVGVGGLEAESVML 226
*************************************************************************** PP
TIGR02333 226 graslmrlpdivgveltgkrqpgitatdivlalteflrkekvvsayleffgegakaltlgdratisnmtpeygat 300
gras+mrlpdivgveltgk qpgit+td+vla+teflrkekvv+aylef+gega +l++gdratisnmtpeygat
lcl|FitnessBrowser__Marino:GFF1973 227 GRASMMRLPDIVGVELTGKLQPGITSTDMVLAITEFLRKEKVVGAYLEFYGEGADSLSVGDRATISNMTPEYGAT 301
*************************************************************************** PP
TIGR02333 301 aamfaideqtidylkltgreeeqvklvetyakaaglwadslkkavyervlkfdlssvvrnlagpsnpharlatsd 375
aamf+id qtidylkltgre++qv+lve +ak +glwads+k+a+yervlkfdls v+r+lagpsnpha l+ts+
lcl|FitnessBrowser__Marino:GFF1973 302 AAMFYIDGQTIDYLKLTGREDDQVALVEKFAKETGLWADSMKNAEYERVLKFDLSKVTRTLAGPSNPHAHLPTSE 376
*************************************************************************** PP
TIGR02333 376 laakgiakeveeeaeglmpdgaviiaaitsctntsnprnvvaagllarnanklglkrkpwvksslapgskvvkly 450
laa+gia+e+e+e g+mpdga iiaaitsctntsnprn+vaagl+arnanklgl+rkpwvk+slapgsk+vk+y
lcl|FitnessBrowser__Marino:GFF1973 377 LAARGIAGEWEQEE-GKMPDGACIIAAITSCTNTSNPRNMVAAGLIARNANKLGLTRKPWVKTSLAPGSKTVKMY 450
***********987.************************************************************ PP
TIGR02333 451 leeagllkeleklgfgivafacttcngmsgaldpviqqeiidrdlyatavlsgnrnfdgrihpyakqaflasppl 525
leea ll+ele+lgfg+vafacttcngmsgaldp+i qei+drdl++tavlsgnrnfdgrihpyakqaflasppl
lcl|FitnessBrowser__Marino:GFF1973 451 LEEAKLLPELEQLGFGVVAFACTTCNGMSGALDPKIAQEIMDRDLFSTAVLSGNRNFDGRIHPYAKQAFLASPPL 525
*************************************************************************** PP
TIGR02333 526 vvayaiagtirfdiekdvlgvdadgkeirlkdiwpsdeeidavvaaavkpeqfrkvyipmfdle.daqkkvsply 599
vvayaiagtirfdiekd+lg+d+dg+++ lkdiwp d+eida+v+++vkpeqfr+ yipmfd+ daq ++ ply
lcl|FitnessBrowser__Marino:GFF1973 526 VVAYAIAGTIRFDIEKDALGYDQDGNPVTLKDIWPDDAEIDAIVKSSVKPEQFRSTYIPMFDITrDAQANTNPLY 600
***************************************************************999********* PP
TIGR02333 600 dwrpmstyirrppywegalagertlkgmrplavlgdnittdhlspsnailldsaageylakmglpeedfnsyath 674
wrp+styirrppyweg + ge+tlkgmrplavl+dnittdhlspsnai+++saageyl+kmg+peedfnsyath
lcl|FitnessBrowser__Marino:GFF1973 601 KWRPQSTYIRRPPYWEGGMVGEKTLKGMRPLAVLPDNITTDHLSPSNAIMMNSAAGEYLHKMGVPEEDFNSYATH 675
*************************************************************************** PP
TIGR02333 675 rgdhltaqratfanpklfnemvked.gkvkqgslariepegkvtrmweaietymnrkqpliiiagadygqgssrd 748
rgdhltaqratfanpklfnemv+++ g+vkqgslariepegkv+rmweaietym+rkqpliiiagadygqgssrd
lcl|FitnessBrowser__Marino:GFF1973 676 RGDHLTAQRATFANPKLFNEMVRDEnGNVKQGSLARIEPEGKVVRMWEAIETYMERKQPLIIIAGADYGQGSSRD 750
***********************988************************************************* PP
TIGR02333 749 waakgvrlagveaivaegferihrtnlvgmgvlplefkpgtnrktlaldgtevydvvgeitpradltlvvtrkng 823
waakgv lagveaivaegferihrtnl+gmgv+pl+f gt rktl++dgte+ydv g+ +pra+ltlv++rkng
lcl|FitnessBrowser__Marino:GFF1973 751 WAAKGVALAGVEAIVAEGFERIHRTNLIGMGVMPLQFEEGTTRKTLGIDGTETYDVEGTPAPRAELTLVIHRKNG 825
*************************************************************************** PP
TIGR02333 824 eklevpvtcrldtaeevsvyeaggvlqrfaqdfle 858
+ +pv crldtaeevs+y aggvlqrfa+dfl+
lcl|FitnessBrowser__Marino:GFF1973 826 STERIPVVCRLDTAEEVSIYSAGGVLQRFAEDFLQ 860
*********************************95 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (858 nodes)
Target sequences: 1 (865 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 0.02s 00:00:00.08 Elapsed: 00:00:00.08
# Mc/sec: 8.42
//
[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