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 199538 SO0343 aconitate hydratase 1 (NCBI ptt file)
Query= SwissProt::Q937N8
(869 letters)
>FitnessBrowser__MR1:199538
Length = 867
Score = 1447 bits (3747), Expect = 0.0
Identities = 722/866 (83%), Positives = 783/866 (90%), Gaps = 6/866 (0%)
Query: 1 MNSANRKPLPGTKLDYFDARAAVEAIQPGAYDKLPYTSRVLAENLVRRCDPATLTDSLLQ 60
MN+ RKPLPGT LDYFD R A+EAI PGAY KLPYTSRVLAENLVRRC+P LT SL Q
Sbjct: 5 MNTQYRKPLPGTALDYFDTREAIEAIAPGAYAKLPYTSRVLAENLVRRCEPEMLTASLKQ 64
Query: 61 LVGRKRDLDFPWFPARVVCHDILGQTALVDLAGLRDAIADQGGDPAKVNPVVPVQLIVDH 120
++ K++LDFPWFPARVVCHDILGQTALVDLAGLRDAIA +GGDPA+VNPVVP QLIVDH
Sbjct: 65 IIESKQELDFPWFPARVVCHDILGQTALVDLAGLRDAIAAKGGDPAQVNPVVPTQLIVDH 124
Query: 121 SLAVECGGFDPDAFAKNRAIEDRRNEDRFHFIDWTKQAFKNVDVIPPGNGIMHQINLEKM 180
SLAVE GGFD DAFAKNRAIEDRRNEDRFHFI+WT++AFKN+DVIP GNGIMHQINLE+M
Sbjct: 125 SLAVEYGGFDKDAFAKNRAIEDRRNEDRFHFINWTQKAFKNIDVIPQGNGIMHQINLERM 184
Query: 181 SPVIHADNGVAYPDTCVGTDSHTPHVDALGVIAIGVGGLEAENVMLGRASWMRLPDIVGV 240
SPVIHA NGVA+PDT VGTDSHTPHVDALGVIAIGVGGLEAE+VMLGRAS+MRLPDI+GV
Sbjct: 185 SPVIHARNGVAFPDTLVGTDSHTPHVDALGVIAIGVGGLEAESVMLGRASYMRLPDIIGV 244
Query: 241 ELTGKRQPGITATDIVLALTEFLRKEKVVGAYLEFRGEGASSLTLGDRATISNMAPEYGA 300
ELTGK QPGITATDIVLALTEFLR +KVV +YLEF GEGA +LTLGDRATISNM PE+GA
Sbjct: 245 ELTGKPQPGITATDIVLALTEFLRAQKVVSSYLEFFGEGAEALTLGDRATISNMTPEFGA 304
Query: 301 TAAMFFIDEQTIDYLRLTGRTDEQLKLVETYARTAGLWADSLKNAEYERVLKFDLSSVVR 360
TAAMF+ID+QT+DYL LTGR EQ+KLVETYA+TAGLW+D LK A Y R L FDLSSVVR
Sbjct: 305 TAAMFYIDQQTLDYLTLTGREAEQVKLVETYAKTAGLWSDDLKQAVYPRTLHFDLSSVVR 364
Query: 361 NMAGPSNPHKRLPTSALAERGIAVDLDKASAQEAEGLMPDGAVIIAAITSCTNTSNPRNV 420
+AGPSNPH R+PTS LA RGI+ +++ GLMPDGAVIIAAITSCTNTSNPRNV
Sbjct: 365 TIAGPSNPHARVPTSELAARGISGEVENEP-----GLMPDGAVIIAAITSCTNTSNPRNV 419
Query: 421 IAAALLARNANARGLARKPWVKSSLAPGSKAVELYLEEANLLPDLEKLGFGIVAFACTTC 480
IAA LLARNANA+GL RKPWVK+SLAPGSKAV+LYLEEANLLP+LE LGFGIV FACTTC
Sbjct: 420 IAAGLLARNANAKGLTRKPWVKTSLAPGSKAVQLYLEEANLLPELESLGFGIVGFACTTC 479
Query: 481 NGMSGALDPKIQQEIIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTI 540
NGMSGALDP IQQE+IDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTI
Sbjct: 480 NGMSGALDPVIQQEVIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTI 539
Query: 541 RFDIEKDVLGTDQDGKPVYLKDIWPSDEEIDAIVAKSVKPEQFRKVYEPMFAITAASGES 600
RFDIEKDVLG D+DGKPV L +IWPSD EIDA++A SVKPEQFRKVYEPMF ++ G+
Sbjct: 540 RFDIEKDVLGLDKDGKPVRLINIWPSDAEIDAVIAASVKPEQFRKVYEPMFDLSVDYGDK 599
Query: 601 VSPLYDWRPQSTYIRRPPYWEGALAGERTLKALRPLAVLGDNITTDHLSPSNAIMLNSAA 660
VSPLYDWRPQSTYIRRPPYWEGALAGERTLK +RPLAVLGDNITTDHLSPSNAIM++SAA
Sbjct: 600 VSPLYDWRPQSTYIRRPPYWEGALAGERTLKGMRPLAVLGDNITTDHLSPSNAIMMDSAA 659
Query: 661 GEYLARMGLPEEDFNSYATHRGDHLTAQRATFANPTLINEMAVVDGQVKKGSLARIEPEG 720
GEYL +MGLPEEDFNSYATHRGDHLTAQRATFANP L NEMA+VDG+VK+GSLARIEPEG
Sbjct: 660 GEYLHKMGLPEEDFNSYATHRGDHLTAQRATFANPKLKNEMAIVDGKVKQGSLARIEPEG 719
Query: 721 KVVRMWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEVIVAEGFERIHRTN 780
V RMWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVE IVAEGFERIHRTN
Sbjct: 720 IVTRMWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEAIVAEGFERIHRTN 779
Query: 781 LIGMGVLPLEFKPGVNRLTLGLDGTETYDVIGERQPRATLTLVVNRKNGERVEVPVTCRL 840
L+GMGVLPLEFK G NR T G+DGTE +DVIG PRA LT+++ RKNGERVEVPVTCRL
Sbjct: 780 LVGMGVLPLEFKAGENRATYGIDGTEVFDVIGSIAPRADLTVIITRKNGERVEVPVTCRL 839
Query: 841 DSDEEVSIYEAGGVL-HFAQDFLESS 865
D+ EEVSIYEAGGVL FAQDFLES+
Sbjct: 840 DTAEEVSIYEAGGVLQRFAQDFLESN 865
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: 2213
Number of extensions: 88
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: 867
Length adjustment: 42
Effective length of query: 827
Effective length of database: 825
Effective search space: 682275
Effective search space used: 682275
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 199538 SO0343 (aconitate hydratase 1 (NCBI ptt file))
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.11610.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 1873.1 0.0 0 1873.0 0.0 1.0 1 lcl|FitnessBrowser__MR1:199538 SO0343 aconitate hydratase 1 (NC
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__MR1:199538 SO0343 aconitate hydratase 1 (NCBI ptt file)
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1873.0 0.0 0 0 1 858 [] 6 863 .. 6 863 .. 1.00
Alignments for each domain:
== domain 1 score: 1873.0 bits; conditional E-value: 0
TIGR02333 1 ntkyrkalpgtdldyfdaraaveaikpgaydklpytsrvlaenlvrrvdpetleaslkqlierkreldfpwyparvvch 79
nt+yrk+lpgt+ldyfd+r+a+eai+pgay+klpytsrvlaenlvrr++pe+l+aslkq+ie+k+eldfpw+parvvch
lcl|FitnessBrowser__MR1:199538 6 NTQYRKPLPGTALDYFDTREAIEAIAPGAYAKLPYTSRVLAENLVRRCEPEMLTASLKQIIESKQELDFPWFPARVVCH 84
89***************************************************************************** PP
TIGR02333 80 dilgqtalvdlaglrdaiaekggdpaqvnpvvetqlivdhslaveyggfdpdafeknraiedrrnedrfhfinwtkkaf 158
dilgqtalvdlaglrdaia+kggdpaqvnpvv+tqlivdhslaveyggfd+daf+knraiedrrnedrfhfinwt+kaf
lcl|FitnessBrowser__MR1:199538 85 DILGQTALVDLAGLRDAIAAKGGDPAQVNPVVPTQLIVDHSLAVEYGGFDKDAFAKNRAIEDRRNEDRFHFINWTQKAF 163
******************************************************************************* PP
TIGR02333 159 knvdvipagngimhqinlekmspvvqvkegvafpdtlvgtdshtphvdalgviaigvggleaetvmlgraslmrlpdiv 237
kn+dvip+gngimhqinle+mspv+++++gvafpdtlvgtdshtphvdalgviaigvggleae+vmlgras+mrlpdi+
lcl|FitnessBrowser__MR1:199538 164 KNIDVIPQGNGIMHQINLERMSPVIHARNGVAFPDTLVGTDSHTPHVDALGVIAIGVGGLEAESVMLGRASYMRLPDII 242
******************************************************************************* PP
TIGR02333 238 gveltgkrqpgitatdivlalteflrkekvvsayleffgegakaltlgdratisnmtpeygataamfaideqtidylkl 316
gveltgk qpgitatdivlalteflr++kvvs+yleffgega+altlgdratisnmtpe+gataamf+id+qt+dyl+l
lcl|FitnessBrowser__MR1:199538 243 GVELTGKPQPGITATDIVLALTEFLRAQKVVSSYLEFFGEGAEALTLGDRATISNMTPEFGATAAMFYIDQQTLDYLTL 321
******************************************************************************* PP
TIGR02333 317 tgreeeqvklvetyakaaglwadslkkavyervlkfdlssvvrnlagpsnpharlatsdlaakgiakeveeeaeglmpd 395
tgre+eqvklvetyak+aglw+d+lk+avy+r+l+fdlssvvr++agpsnphar++ts+laa+gi++eve+e+ glmpd
lcl|FitnessBrowser__MR1:199538 322 TGREAEQVKLVETYAKTAGLWSDDLKQAVYPRTLHFDLSSVVRTIAGPSNPHARVPTSELAARGISGEVENEP-GLMPD 399
*************************************************************************.***** PP
TIGR02333 396 gaviiaaitsctntsnprnvvaagllarnanklglkrkpwvksslapgskvvklyleeagllkeleklgfgivafactt 474
gaviiaaitsctntsnprnv+aagllarnan++gl+rkpwvk+slapgsk+v+lyleea+ll+ele+lgfgiv+factt
lcl|FitnessBrowser__MR1:199538 400 GAVIIAAITSCTNTSNPRNVIAAGLLARNANAKGLTRKPWVKTSLAPGSKAVQLYLEEANLLPELESLGFGIVGFACTT 478
******************************************************************************* PP
TIGR02333 475 cngmsgaldpviqqeiidrdlyatavlsgnrnfdgrihpyakqaflaspplvvayaiagtirfdiekdvlgvdadgkei 553
cngmsgaldpviqqe+idrdlyatavlsgnrnfdgrihpyakqaflaspplvvayaiagtirfdiekdvlg+d+dgk++
lcl|FitnessBrowser__MR1:199538 479 CNGMSGALDPVIQQEVIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTIRFDIEKDVLGLDKDGKPV 557
******************************************************************************* PP
TIGR02333 554 rlkdiwpsdeeidavvaaavkpeqfrkvyipmfdle.daqkkvsplydwrpmstyirrppywegalagertlkgmrpla 631
rl++iwpsd+eidav+aa+vkpeqfrkvy+pmfdl+ d+++kvsplydwrp+styirrppywegalagertlkgmrpla
lcl|FitnessBrowser__MR1:199538 558 RLINIWPSDAEIDAVIAASVKPEQFRKVYEPMFDLSvDYGDKVSPLYDWRPQSTYIRRPPYWEGALAGERTLKGMRPLA 636
******************************************************************************* PP
TIGR02333 632 vlgdnittdhlspsnailldsaageylakmglpeedfnsyathrgdhltaqratfanpklfnemvkedgkvkqgslari 710
vlgdnittdhlspsnai++dsaageyl+kmglpeedfnsyathrgdhltaqratfanpkl+nem+++dgkvkqgslari
lcl|FitnessBrowser__MR1:199538 637 VLGDNITTDHLSPSNAIMMDSAAGEYLHKMGLPEEDFNSYATHRGDHLTAQRATFANPKLKNEMAIVDGKVKQGSLARI 715
******************************************************************************* PP
TIGR02333 711 epegkvtrmweaietymnrkqpliiiagadygqgssrdwaakgvrlagveaivaegferihrtnlvgmgvlplefkpgt 789
epeg+vtrmweaietym+rkqpliiiagadygqgssrdwaakgvrlagveaivaegferihrtnlvgmgvlplefk+g+
lcl|FitnessBrowser__MR1:199538 716 EPEGIVTRMWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEAIVAEGFERIHRTNLVGMGVLPLEFKAGE 794
******************************************************************************* PP
TIGR02333 790 nrktlaldgtevydvvgeitpradltlvvtrkngeklevpvtcrldtaeevsvyeaggvlqrfaqdfle 858
nr+t+++dgtev+dv+g+i+pradlt+++trknge++evpvtcrldtaeevs+yeaggvlqrfaqdfle
lcl|FitnessBrowser__MR1:199538 795 NRATYGIDGTEVFDVIGSIAPRADLTVIITRKNGERVEVPVTCRLDTAEEVSIYEAGGVLQRFAQDFLE 863
*******************************************************************97 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (858 nodes)
Target sequences: 1 (867 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: 0.05u 0.02s 00:00:00.07 Elapsed: 00:00:00.06
# Mc/sec: 11.56
//
[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