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 HSERO_RS11425 HSERO_RS11425 aconitate hydratase
Query= SwissProt::Q937N8
(869 letters)
>FitnessBrowser__HerbieS:HSERO_RS11425
Length = 873
Score = 1476 bits (3821), Expect = 0.0
Identities = 739/867 (85%), Positives = 790/867 (91%), Gaps = 7/867 (0%)
Query: 1 MNSANRKPLPGTKLDYFDARAAVEAIQPGAYDKLPYTSRVLAENLVRRCDPATLTDSLLQ 60
MN+ RK LPGT+LDYFDARAAVEAI+PGA+D LPYTSRVLAENLVRRCDPATLTDSL Q
Sbjct: 1 MNTQYRKQLPGTRLDYFDARAAVEAIRPGAWDTLPYTSRVLAENLVRRCDPATLTDSLRQ 60
Query: 61 LVGRKRDLDFPWFPARVVCHDILGQTALVDLAGLRDAIADQGGDPAKVNPVVPVQLIVDH 120
L+ RKR+LDFPWFPARVVCHDILGQTALVDLAGLRDAIAD GGDPAKVNPVVPVQLIVDH
Sbjct: 61 LIERKRELDFPWFPARVVCHDILGQTALVDLAGLRDAIADMGGDPAKVNPVVPVQLIVDH 120
Query: 121 SLAVECGGFDPDAFAKNRAIEDRRNEDRFHFIDWTKQAFKNVDVIPPGNGIMHQINLEKM 180
SLAVECGG DP AF KNRAIEDRRNEDRFHFIDWTK AF+NVDVIPPGNGIMHQINLEKM
Sbjct: 121 SLAVECGGDDPQAFVKNRAIEDRRNEDRFHFIDWTKLAFENVDVIPPGNGIMHQINLEKM 180
Query: 181 SPVIHADNGVAYPDTCVGTDSHTPHVDALGVIAIGVGGLEAENVMLGRASWMRLPDIVGV 240
SPVIHA +GVA+PDT VGTDSHTPHVDALGVIAIGVGGLEAENVMLGRASWMRLPDI+GV
Sbjct: 181 SPVIHAKDGVAFPDTLVGTDSHTPHVDALGVIAIGVGGLEAENVMLGRASWMRLPDIIGV 240
Query: 241 ELTGKRQPGITATDIVLALTEFLRKEKVVGAYLEFRGEGASSLTLGDRATISNMAPEYGA 300
ELTG+RQPGITATDIVL+LTEFLRK+KVVGAYLEF G+GA+SLTLGDRATISNMAPEYGA
Sbjct: 241 ELTGRRQPGITATDIVLSLTEFLRKQKVVGAYLEFYGDGAASLTLGDRATISNMAPEYGA 300
Query: 301 TAAMFFIDEQTIDYLRLTGRTDEQLKLVETYARTAGLWADSLKNAEYERVLKFDLSSVVR 360
TAAMF ID+QTIDYL+LTGR DEQ+KLVETYA+ AGLW+D+L EYERVL+FDLS+VVR
Sbjct: 301 TAAMFSIDQQTIDYLKLTGREDEQVKLVETYAKEAGLWSDTLAKVEYERVLRFDLSTVVR 360
Query: 361 NMAGPSNPHKRLPTSALAERGIAVDLDKASAQEAEGLMPDGAVIIAAITSCTNTSNPRNV 420
+AGPSNPHKRLP S LA +GIA + G MPDGAVIIAAITSCTNTSNPRNV
Sbjct: 361 TLAGPSNPHKRLPVSELAAQGIA-----GKVENEPGKMPDGAVIIAAITSCTNTSNPRNV 415
Query: 421 IAAALLARNANARGLARKPWVKSSLAPGSKAVELYLEEANLLPDLEKLGFGIVAFACTTC 480
IAA LLARNAN GLARKPWVKSSLAPGSKAVELYLEEA L DLEKLGFGIVAFACTTC
Sbjct: 416 IAAGLLARNANRLGLARKPWVKSSLAPGSKAVELYLEEAGLTADLEKLGFGIVAFACTTC 475
Query: 481 NGMSGALDPKIQQEIIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTI 540
NGMSGALDPKIQQEIIDRDLY+TAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTI
Sbjct: 476 NGMSGALDPKIQQEIIDRDLYSTAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTI 535
Query: 541 RFDIEKDVLGTDQDGKPVYLKDIWPSDEEIDAIVAKSVKPEQFRKVYEPMFAITAASGES 600
RFDIE+DVLG +G+ + LKDIWPSDEEIDA+V +VKP+QFR VY PMFA +S
Sbjct: 536 RFDIEQDVLGVTAEGREIRLKDIWPSDEEIDAVVTAAVKPQQFRNVYTPMFAARVDRSQS 595
Query: 601 VSPLYDWRPQSTYIRRPPYWEGALAGERTLKALRPLAVLGDNITTDHLSPSNAIMLNSAA 660
VSPLYDWRPQSTYIRRPPYWEGALAGERTL +RPLAVLGDNITTDHLSPSNAI+L+SAA
Sbjct: 596 VSPLYDWRPQSTYIRRPPYWEGALAGERTLSGMRPLAVLGDNITTDHLSPSNAILLDSAA 655
Query: 661 GEYLARMGLPEEDFNSYATHRGDHLTAQRATFANPTLINEMA-VVDGQVKKGSLARIEPE 719
GEYLA+MGLPEEDFNSYATHRGDHLTAQRATFANP L NEM DG V++GSLAR+EPE
Sbjct: 656 GEYLAKMGLPEEDFNSYATHRGDHLTAQRATFANPKLFNEMVKKADGSVQQGSLARLEPE 715
Query: 720 GKVVRMWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEVIVAEGFERIHRT 779
GKV+RMWE IETYM+RKQPLIIIAGADYGQGSSRDWAAKGVRLAGVE IVAEGFERIHRT
Sbjct: 716 GKVMRMWETIETYMERKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEAIVAEGFERIHRT 775
Query: 780 NLIGMGVLPLEFKPGVNRLTLGLDGTETYDVIGERQPRATLTLVVNRKNGERVEVPVTCR 839
NLIGMGVLPLEFK G NR T +DGTETYDVIG+R+PRA LTLV++RKNGERVEVPVTCR
Sbjct: 776 NLIGMGVLPLEFKAGENRNTYAIDGTETYDVIGQRRPRADLTLVIHRKNGERVEVPVTCR 835
Query: 840 LDSDEEVSIYEAGGVL-HFAQDFLESS 865
LD+ EEVSIYEAGGVL FAQDFLE+S
Sbjct: 836 LDTAEEVSIYEAGGVLQRFAQDFLEAS 862
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: 2276
Number of extensions: 102
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: 873
Length adjustment: 42
Effective length of query: 827
Effective length of database: 831
Effective search space: 687237
Effective search space used: 687237
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 HSERO_RS11425 HSERO_RS11425 (aconitate hydratase)
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.14723.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 1816.5 0.0 0 1816.3 0.0 1.0 1 lcl|FitnessBrowser__HerbieS:HSERO_RS11425 HSERO_RS11425 aconitate hydratas
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__HerbieS:HSERO_RS11425 HSERO_RS11425 aconitate hydratase
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1816.3 0.0 0 0 1 858 [] 2 860 .. 2 860 .. 1.00
Alignments for each domain:
== domain 1 score: 1816.3 bits; conditional E-value: 0
TIGR02333 1 ntkyrkalpgtdldyfdaraaveaikpgaydklpytsrvlaenlvrrvdpetleaslkqlierkreld 68
nt+yrk+lpgt ldyfdaraaveai+pga+d+lpytsrvlaenlvrr+dp+tl++sl+qlierkreld
lcl|FitnessBrowser__HerbieS:HSERO_RS11425 2 NTQYRKQLPGTRLDYFDARAAVEAIRPGAWDTLPYTSRVLAENLVRRCDPATLTDSLRQLIERKRELD 69
89****************************************************************** PP
TIGR02333 69 fpwyparvvchdilgqtalvdlaglrdaiaekggdpaqvnpvvetqlivdhslaveyggfdpdafekn 136
fpw+parvvchdilgqtalvdlaglrdaia+ ggdpa+vnpvv++qlivdhslave+gg dp+af kn
lcl|FitnessBrowser__HerbieS:HSERO_RS11425 70 FPWFPARVVCHDILGQTALVDLAGLRDAIADMGGDPAKVNPVVPVQLIVDHSLAVECGGDDPQAFVKN 137
******************************************************************** PP
TIGR02333 137 raiedrrnedrfhfinwtkkafknvdvipagngimhqinlekmspvvqvkegvafpdtlvgtdshtph 204
raiedrrnedrfhfi+wtk af+nvdvip+gngimhqinlekmspv+++k+gvafpdtlvgtdshtph
lcl|FitnessBrowser__HerbieS:HSERO_RS11425 138 RAIEDRRNEDRFHFIDWTKLAFENVDVIPPGNGIMHQINLEKMSPVIHAKDGVAFPDTLVGTDSHTPH 205
******************************************************************** PP
TIGR02333 205 vdalgviaigvggleaetvmlgraslmrlpdivgveltgkrqpgitatdivlalteflrkekvvsayl 272
vdalgviaigvggleae+vmlgras+mrlpdi+gveltg+rqpgitatdivl+lteflrk+kvv+ayl
lcl|FitnessBrowser__HerbieS:HSERO_RS11425 206 VDALGVIAIGVGGLEAENVMLGRASWMRLPDIIGVELTGRRQPGITATDIVLSLTEFLRKQKVVGAYL 273
******************************************************************** PP
TIGR02333 273 effgegakaltlgdratisnmtpeygataamfaideqtidylkltgreeeqvklvetyakaaglwads 340
ef+g+ga +ltlgdratisnm+peygataamf id+qtidylkltgre+eqvklvetyak aglw+d+
lcl|FitnessBrowser__HerbieS:HSERO_RS11425 274 EFYGDGAASLTLGDRATISNMAPEYGATAAMFSIDQQTIDYLKLTGREDEQVKLVETYAKEAGLWSDT 341
******************************************************************** PP
TIGR02333 341 lkkavyervlkfdlssvvrnlagpsnpharlatsdlaakgiakeveeeaeglmpdgaviiaaitsctn 408
l k +yervl+fdls+vvr+lagpsnph+rl+ s+laa+gia++ve+e+ g+mpdgaviiaaitsctn
lcl|FitnessBrowser__HerbieS:HSERO_RS11425 342 LAKVEYERVLRFDLSTVVRTLAGPSNPHKRLPVSELAAQGIAGKVENEP-GKMPDGAVIIAAITSCTN 408
*************************************************.****************** PP
TIGR02333 409 tsnprnvvaagllarnanklglkrkpwvksslapgskvvklyleeagllkeleklgfgivafacttcn 476
tsnprnv+aagllarnan+lgl rkpwvksslapgsk+v+lyleeagl ++leklgfgivafacttcn
lcl|FitnessBrowser__HerbieS:HSERO_RS11425 409 TSNPRNVIAAGLLARNANRLGLARKPWVKSSLAPGSKAVELYLEEAGLTADLEKLGFGIVAFACTTCN 476
******************************************************************** PP
TIGR02333 477 gmsgaldpviqqeiidrdlyatavlsgnrnfdgrihpyakqaflaspplvvayaiagtirfdiekdvl 544
gmsgaldp+iqqeiidrdly+tavlsgnrnfdgrihpyakqaflaspplvvayaiagtirfdie+dvl
lcl|FitnessBrowser__HerbieS:HSERO_RS11425 477 GMSGALDPKIQQEIIDRDLYSTAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTIRFDIEQDVL 544
******************************************************************** PP
TIGR02333 545 gvdadgkeirlkdiwpsdeeidavvaaavkpeqfrkvyipmfdle.daqkkvsplydwrpmstyirrp 611
gv a+g+eirlkdiwpsdeeidavv+aavkp+qfr+vy pmf+ d++++vsplydwrp+styirrp
lcl|FitnessBrowser__HerbieS:HSERO_RS11425 545 GVTAEGREIRLKDIWPSDEEIDAVVTAAVKPQQFRNVYTPMFAARvDRSQSVSPLYDWRPQSTYIRRP 612
*******************************************999********************** PP
TIGR02333 612 pywegalagertlkgmrplavlgdnittdhlspsnailldsaageylakmglpeedfnsyathrgdhl 679
pywegalagertl gmrplavlgdnittdhlspsnailldsaageylakmglpeedfnsyathrgdhl
lcl|FitnessBrowser__HerbieS:HSERO_RS11425 613 PYWEGALAGERTLSGMRPLAVLGDNITTDHLSPSNAILLDSAAGEYLAKMGLPEEDFNSYATHRGDHL 680
******************************************************************** PP
TIGR02333 680 taqratfanpklfnemvked.gkvkqgslariepegkvtrmweaietymnrkqpliiiagadygqgss 746
taqratfanpklfnemvk+ g+v+qgslar+epegkv+rmwe+ietym+rkqpliiiagadygqgss
lcl|FitnessBrowser__HerbieS:HSERO_RS11425 681 TAQRATFANPKLFNEMVKKAdGSVQQGSLARLEPEGKVMRMWETIETYMERKQPLIIIAGADYGQGSS 748
*****************9766*********************************************** PP
TIGR02333 747 rdwaakgvrlagveaivaegferihrtnlvgmgvlplefkpgtnrktlaldgtevydvvgeitpradl 814
rdwaakgvrlagveaivaegferihrtnl+gmgvlplefk+g+nr+t+a+dgte+ydv+g+++pradl
lcl|FitnessBrowser__HerbieS:HSERO_RS11425 749 RDWAAKGVRLAGVEAIVAEGFERIHRTNLIGMGVLPLEFKAGENRNTYAIDGTETYDVIGQRRPRADL 816
******************************************************************** PP
TIGR02333 815 tlvvtrkngeklevpvtcrldtaeevsvyeaggvlqrfaqdfle 858
tlv++rknge++evpvtcrldtaeevs+yeaggvlqrfaqdfle
lcl|FitnessBrowser__HerbieS:HSERO_RS11425 817 TLVIHRKNGERVEVPVTCRLDTAEEVSIYEAGGVLQRFAQDFLE 860
******************************************97 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (858 nodes)
Target sequences: 1 (873 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: 00:00:00.07
# Mc/sec: 9.51
//
[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