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 GFF4113 PS417_21070 aconitate hydratase
Query= SwissProt::Q937N8
(869 letters)
>FitnessBrowser__WCS417:GFF4113
Length = 864
Score = 1441 bits (3729), Expect = 0.0
Identities = 730/870 (83%), Positives = 779/870 (89%), Gaps = 7/870 (0%)
Query: 1 MNSANRKPLPGTKLDYFDARAAVEAIQPGAYDKLPYTSRVLAENLVRRCDPATLTDSLLQ 60
MN+ RKPLPG++LDYFDARAAV+AI PGAY LPYTSRVLAENLVRRCDPATL SL Q
Sbjct: 1 MNTEFRKPLPGSRLDYFDARAAVDAISPGAYATLPYTSRVLAENLVRRCDPATLNASLSQ 60
Query: 61 LVGRKRDLDFPWFPARVVCHDILGQTALVDLAGLRDAIADQGGDPAKVNPVVPVQLIVDH 120
L+ RKRDLDFPWFPARVVCHDILGQTALVDLAGLRDAIA QGGDPA+VNPVVP QLIVDH
Sbjct: 61 LIERKRDLDFPWFPARVVCHDILGQTALVDLAGLRDAIALQGGDPAQVNPVVPTQLIVDH 120
Query: 121 SLAVECGGFDPDAFAKNRAIEDRRNEDRFHFIDWTKQAFKNVDVIPPGNGIMHQINLEKM 180
SLAVE GGFDPDAF KNRAIEDRRNEDRFHFI+WTK+AFKNVDVIPPGNGIMHQINLEKM
Sbjct: 121 SLAVEAGGFDPDAFEKNRAIEDRRNEDRFHFIEWTKKAFKNVDVIPPGNGIMHQINLEKM 180
Query: 181 SPVIHADNGVAYPDTCVGTDSHTPHVDALGVIAIGVGGLEAENVMLGRASWMRLPDIVGV 240
SPVI +GVA+PDTCVGTDSHTPHVDALGVIAIGVGGLEAE+VMLGRASWMRLP+ VGV
Sbjct: 181 SPVIQVRDGVAFPDTCVGTDSHTPHVDALGVIAIGVGGLEAESVMLGRASWMRLPESVGV 240
Query: 241 ELTGKRQPGITATDIVLALTEFLRKEKVVGAYLEFRGEGASSLTLGDRATISNMAPEYGA 300
ELTGK PGITATD+VLALTEFLRK+KVVGA+LEF GEGAS+LTLGDRATISNMAPEYGA
Sbjct: 241 ELTGKLLPGITATDMVLALTEFLRKQKVVGAWLEFFGEGASALTLGDRATISNMAPEYGA 300
Query: 301 TAAMFFIDEQTIDYLRLTGRTDEQLKLVETYARTAGLWADSLKNAEYERVLKFDLSSVVR 360
TAAMF+ID+QTI YL+LTGR DEQ+ LVE YAR GLWAD LK A+YER L FDLSSVVR
Sbjct: 301 TAAMFYIDQQTIAYLKLTGREDEQVTLVEQYARHTGLWADDLKGAQYERGLTFDLSSVVR 360
Query: 361 NMAGPSNPHKRLPTSALAERGIAVDLDKASAQEAEGLMPDGAVIIAAITSCTNTSNPRNV 420
NMAGPSNPH R+ TS LA +GI+ D E G MPDGAVIIAAITSCTNTSNPRNV
Sbjct: 361 NMAGPSNPHARVATSDLASKGISGQWD-----EVPGQMPDGAVIIAAITSCTNTSNPRNV 415
Query: 421 IAAALLARNANARGLARKPWVKSSLAPGSKAVELYLEEANLLPDLEKLGFGIVAFACTTC 480
IAA LLARNAN GL RKPWVKSSLAPGSK V +YLEEA L +LEKLGFG+VAFACTTC
Sbjct: 416 IAAGLLARNANKLGLTRKPWVKSSLAPGSKTVAMYLEEAGLGHELEKLGFGVVAFACTTC 475
Query: 481 NGMSGALDPKIQQEIIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTI 540
NGMSGALDP IQQEIIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTI
Sbjct: 476 NGMSGALDPVIQQEIIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTI 535
Query: 541 RFDIEKDVLGTDQDGKPVYLKDIWPSDEEIDAIVAKSVKPEQFRKVYEPMFAITAASGES 600
RFDIEKDVLG D +GK + L+DIWPSDEEIDA+V SVKPEQFR VY PMFAI +G
Sbjct: 536 RFDIEKDVLGLDANGKEIRLQDIWPSDEEIDAVVKASVKPEQFRAVYIPMFAIHEDTGPK 595
Query: 601 VSPLYDWRPQSTYIRRPPYWEGALAGERTLKALRPLAVLGDNITTDHLSPSNAIMLNSAA 660
V+PLYDWRPQSTYIRRPPYWEGALAG R LK +RPLAVL DNITTDHLSPSNAIML+SAA
Sbjct: 596 VAPLYDWRPQSTYIRRPPYWEGALAGARPLKGMRPLAVLPDNITTDHLSPSNAIMLDSAA 655
Query: 661 GEYLARMGLPEEDFNSYATHRGDHLTAQRATFANPTLINEMAVVDGQVKKGSLARIEPEG 720
GEYLA+MGLPE DFNSYATHRGDHLTAQRATFANP L NEM V +G+VK+GSLARIEPEG
Sbjct: 656 GEYLAKMGLPEVDFNSYATHRGDHLTAQRATFANPKLFNEMVVENGKVKQGSLARIEPEG 715
Query: 721 KVVRMWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEVIVAEGFERIHRTN 780
+V RMWEAIETYM+RKQPLIIIAGADYGQGSSRDWAAKGVRLAGVE I AEGFERIHRTN
Sbjct: 716 QVTRMWEAIETYMERKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEAIAAEGFERIHRTN 775
Query: 781 LIGMGVLPLEFKPGVNRLTLGLDGTETYDVIGERQPRATLTLVVNRKNGERVEVPVTCRL 840
L+GMGVLPLEF PG +R TL +DG+ETYDV+G R PRA LTLV+NRKNGERVEVPVTCRL
Sbjct: 776 LVGMGVLPLEFLPGTDRHTLKIDGSETYDVVGARTPRAQLTLVINRKNGERVEVPVTCRL 835
Query: 841 DSDEEVSIYEAGGVL-HFAQDFLESSRATA 869
D+ EEVSIYEAGGVL FAQDFLES+ ATA
Sbjct: 836 DTAEEVSIYEAGGVLQRFAQDFLESA-ATA 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: 2182
Number of extensions: 84
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: 864
Length adjustment: 42
Effective length of query: 827
Effective length of database: 822
Effective search space: 679794
Effective search space used: 679794
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 GFF4113 PS417_21070 (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.20851.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 1821.2 0.0 0 1821.1 0.0 1.0 1 lcl|FitnessBrowser__WCS417:GFF4113 PS417_21070 aconitate hydratase
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__WCS417:GFF4113 PS417_21070 aconitate hydratase
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1821.1 0.0 0 0 1 858 [] 2 859 .. 2 859 .. 1.00
Alignments for each domain:
== domain 1 score: 1821.1 bits; conditional E-value: 0
TIGR02333 1 ntkyrkalpgtdldyfdaraaveaikpgaydklpytsrvlaenlvrrvdpetleaslkqlierkreldfpwypar 75
nt++rk+lpg+ ldyfdaraav+ai pgay++lpytsrvlaenlvrr+dp+tl+asl+qlierkr+ldfpw+par
lcl|FitnessBrowser__WCS417:GFF4113 2 NTEFRKPLPGSRLDYFDARAAVDAISPGAYATLPYTSRVLAENLVRRCDPATLNASLSQLIERKRDLDFPWFPAR 76
899************************************************************************ PP
TIGR02333 76 vvchdilgqtalvdlaglrdaiaekggdpaqvnpvvetqlivdhslaveyggfdpdafeknraiedrrnedrfhf 150
vvchdilgqtalvdlaglrdaia +ggdpaqvnpvv+tqlivdhslave ggfdpdafeknraiedrrnedrfhf
lcl|FitnessBrowser__WCS417:GFF4113 77 VVCHDILGQTALVDLAGLRDAIALQGGDPAQVNPVVPTQLIVDHSLAVEAGGFDPDAFEKNRAIEDRRNEDRFHF 151
*************************************************************************** PP
TIGR02333 151 inwtkkafknvdvipagngimhqinlekmspvvqvkegvafpdtlvgtdshtphvdalgviaigvggleaetvml 225
i+wtkkafknvdvip+gngimhqinlekmspv+qv++gvafpdt+vgtdshtphvdalgviaigvggleae+vml
lcl|FitnessBrowser__WCS417:GFF4113 152 IEWTKKAFKNVDVIPPGNGIMHQINLEKMSPVIQVRDGVAFPDTCVGTDSHTPHVDALGVIAIGVGGLEAESVML 226
*************************************************************************** PP
TIGR02333 226 graslmrlpdivgveltgkrqpgitatdivlalteflrkekvvsayleffgegakaltlgdratisnmtpeygat 300
gras+mrlp+ vgveltgk pgitatd+vlalteflrk+kvv+a+leffgega altlgdratisnm+peygat
lcl|FitnessBrowser__WCS417:GFF4113 227 GRASWMRLPESVGVELTGKLLPGITATDMVLALTEFLRKQKVVGAWLEFFGEGASALTLGDRATISNMAPEYGAT 301
*************************************************************************** PP
TIGR02333 301 aamfaideqtidylkltgreeeqvklvetyakaaglwadslkkavyervlkfdlssvvrnlagpsnpharlatsd 375
aamf+id+qti ylkltgre+eqv lve ya+ +glwad+lk a+yer l+fdlssvvrn+agpsnphar+atsd
lcl|FitnessBrowser__WCS417:GFF4113 302 AAMFYIDQQTIAYLKLTGREDEQVTLVEQYARHTGLWADDLKGAQYERGLTFDLSSVVRNMAGPSNPHARVATSD 376
*************************************************************************** PP
TIGR02333 376 laakgiakeveeeaeglmpdgaviiaaitsctntsnprnvvaagllarnanklglkrkpwvksslapgskvvkly 450
la+kgi+++++e++ g+mpdgaviiaaitsctntsnprnv+aagllarnanklgl+rkpwvksslapgsk+v +y
lcl|FitnessBrowser__WCS417:GFF4113 377 LASKGISGQWDEVP-GQMPDGAVIIAAITSCTNTSNPRNVIAAGLLARNANKLGLTRKPWVKSSLAPGSKTVAMY 450
**************.************************************************************ PP
TIGR02333 451 leeagllkeleklgfgivafacttcngmsgaldpviqqeiidrdlyatavlsgnrnfdgrihpyakqaflasppl 525
leeagl +eleklgfg+vafacttcngmsgaldpviqqeiidrdlyatavlsgnrnfdgrihpyakqaflasppl
lcl|FitnessBrowser__WCS417:GFF4113 451 LEEAGLGHELEKLGFGVVAFACTTCNGMSGALDPVIQQEIIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPL 525
*************************************************************************** PP
TIGR02333 526 vvayaiagtirfdiekdvlgvdadgkeirlkdiwpsdeeidavvaaavkpeqfrkvyipmfdle.daqkkvsply 599
vvayaiagtirfdiekdvlg+da+gkeirl+diwpsdeeidavv+a+vkpeqfr vyipmf+++ d++ kv+ply
lcl|FitnessBrowser__WCS417:GFF4113 526 VVAYAIAGTIRFDIEKDVLGLDANGKEIRLQDIWPSDEEIDAVVKASVKPEQFRAVYIPMFAIHeDTGPKVAPLY 600
***************************************************************989********* PP
TIGR02333 600 dwrpmstyirrppywegalagertlkgmrplavlgdnittdhlspsnailldsaageylakmglpeedfnsyath 674
dwrp+styirrppywegalag r lkgmrplavl+dnittdhlspsnai+ldsaageylakmglpe dfnsyath
lcl|FitnessBrowser__WCS417:GFF4113 601 DWRPQSTYIRRPPYWEGALAGARPLKGMRPLAVLPDNITTDHLSPSNAIMLDSAAGEYLAKMGLPEVDFNSYATH 675
*************************************************************************** PP
TIGR02333 675 rgdhltaqratfanpklfnemvkedgkvkqgslariepegkvtrmweaietymnrkqpliiiagadygqgssrdw 749
rgdhltaqratfanpklfnemv e+gkvkqgslariepeg+vtrmweaietym+rkqpliiiagadygqgssrdw
lcl|FitnessBrowser__WCS417:GFF4113 676 RGDHLTAQRATFANPKLFNEMVVENGKVKQGSLARIEPEGQVTRMWEAIETYMERKQPLIIIAGADYGQGSSRDW 750
*************************************************************************** PP
TIGR02333 750 aakgvrlagveaivaegferihrtnlvgmgvlplefkpgtnrktlaldgtevydvvgeitpradltlvvtrknge 824
aakgvrlagveai aegferihrtnlvgmgvlplef pgt+r+tl++dg+e+ydvvg++tpra+ltlv++rknge
lcl|FitnessBrowser__WCS417:GFF4113 751 AAKGVRLAGVEAIAAEGFERIHRTNLVGMGVLPLEFLPGTDRHTLKIDGSETYDVVGARTPRAQLTLVINRKNGE 825
*************************************************************************** PP
TIGR02333 825 klevpvtcrldtaeevsvyeaggvlqrfaqdfle 858
++evpvtcrldtaeevs+yeaggvlqrfaqdfle
lcl|FitnessBrowser__WCS417:GFF4113 826 RVEVPVTCRLDTAEEVSIYEAGGVLQRFAQDFLE 859
********************************97 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (858 nodes)
Target sequences: 1 (864 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: 11.25
//
[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