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 BPHYT_RS30145 BPHYT_RS30145 aconitate hydratase
Query= SwissProt::Q937N8
(869 letters)
>FitnessBrowser__BFirm:BPHYT_RS30145
Length = 865
Score = 1460 bits (3780), Expect = 0.0
Identities = 725/870 (83%), Positives = 790/870 (90%), Gaps = 6/870 (0%)
Query: 1 MNSANRKPLPGTKLDYFDARAAVEAIQPGAYDKLPYTSRVLAENLVRRCDPATLTDSLLQ 60
MN+ANRK LPGT+LD+FD RAAV+AIQPGAYDKLPYTSRVLAENLVRRCDP TLT SL Q
Sbjct: 1 MNTANRKRLPGTQLDFFDTRAAVDAIQPGAYDKLPYTSRVLAENLVRRCDPVTLTASLKQ 60
Query: 61 LVGRKRDLDFPWFPARVVCHDILGQTALVDLAGLRDAIADQGGDPAKVNPVVPVQLIVDH 120
++ RKR+LDFPWFPARVVCHDILGQTALVDLAGLRDAIA QGGDPA VNPVVP QL+VDH
Sbjct: 61 IIERKRELDFPWFPARVVCHDILGQTALVDLAGLRDAIAAQGGDPALVNPVVPTQLVVDH 120
Query: 121 SLAVECGGFDPDAFAKNRAIEDRRNEDRFHFIDWTKQAFKNVDVIPPGNGIMHQINLEKM 180
SLAVECGGFDPDAFAKNRAIEDRRNEDRF FI+WTK+AF+NVDVIPPGNGI+HQINLE+M
Sbjct: 121 SLAVECGGFDPDAFAKNRAIEDRRNEDRFDFINWTKRAFRNVDVIPPGNGILHQINLERM 180
Query: 181 SPVIHADNGVAYPDTCVGTDSHTPHVDALGVIAIGVGGLEAENVMLGRASWMRLPDIVGV 240
SPV+ +GVA+PDT VGTDSHTP VDALGVIAIGVGGLEAE+VMLGRAS+MRLPDIVGV
Sbjct: 181 SPVVQVKDGVAFPDTLVGTDSHTPMVDALGVIAIGVGGLEAESVMLGRASYMRLPDIVGV 240
Query: 241 ELTGKRQPGITATDIVLALTEFLRKEKVVGAYLEFRGEGASSLTLGDRATISNMAPEYGA 300
ELTGK GITATD+VL+LTEFLRKEKVVGAYLEF G G + LTLGDRATI+NMAPE+GA
Sbjct: 241 ELTGKPAEGITATDVVLSLTEFLRKEKVVGAYLEFYGTGTAKLTLGDRATIANMAPEFGA 300
Query: 301 TAAMFFIDEQTIDYLRLTGRTDEQLKLVETYARTAGLWADSLKNAEYERVLKFDLSSVVR 360
TAAMF IDEQTI YL+LTGR DE +K VETYA+ GLWADSL NAEYERVLKFDLS+VVR
Sbjct: 301 TAAMFSIDEQTIKYLKLTGRDDELVKRVETYAKKTGLWADSLVNAEYERVLKFDLSTVVR 360
Query: 361 NMAGPSNPHKRLPTSALAERGIAVDLDKASAQEAEGLMPDGAVIIAAITSCTNTSNPRNV 420
+AGPSNPH+RLP S LA RGI+ + GLMPDGAVIIAAITSCTNT+NPRN+
Sbjct: 361 TLAGPSNPHRRLPVSELAARGIS-----GKVENEPGLMPDGAVIIAAITSCTNTNNPRNM 415
Query: 421 IAAALLARNANARGLARKPWVKSSLAPGSKAVELYLEEANLLPDLEKLGFGIVAFACTTC 480
IAA LLARNAN RGL RKPW K+SLAPGSKAV LYLEEA LLP+LE+LGFG+VA+ACT+C
Sbjct: 416 IAAGLLARNANRRGLTRKPWAKTSLAPGSKAVTLYLEEAGLLPELEQLGFGVVAYACTSC 475
Query: 481 NGMSGALDPKIQQEIIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTI 540
NGMSGALDP IQ+EI++RDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTI
Sbjct: 476 NGMSGALDPVIQKEIVERDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTI 535
Query: 541 RFDIEKDVLGTDQDGKPVYLKDIWPSDEEIDAIVAKSVKPEQFRKVYEPMFAITAASGES 600
RFDIEKDVLG D DG+ V LKDIWP+D EIDAIVA SVKPEQFRKVYEPMFA++ +GE
Sbjct: 536 RFDIEKDVLGIDADGQAVTLKDIWPTDAEIDAIVASSVKPEQFRKVYEPMFAVSVDTGEK 595
Query: 601 VSPLYDWRPQSTYIRRPPYWEGALAGERTLKALRPLAVLGDNITTDHLSPSNAIMLNSAA 660
PLY+WRP STYIRRPPYWEGALAGERTLK +RPLAVLGDNITTDHLSPSNAI+ +SA+
Sbjct: 596 ADPLYNWRPMSTYIRRPPYWEGALAGERTLKGMRPLAVLGDNITTDHLSPSNAILADSAS 655
Query: 661 GEYLARMGLPEEDFNSYATHRGDHLTAQRATFANPTLINEMAVVDGQVKKGSLARIEPEG 720
GEYLA+MGLPEEDFNSYATHRGDHLTAQRATFANPTL NEM + DG+VK GSLARIEPEG
Sbjct: 656 GEYLAKMGLPEEDFNSYATHRGDHLTAQRATFANPTLKNEMVLEDGKVKAGSLARIEPEG 715
Query: 721 KVVRMWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEVIVAEGFERIHRTN 780
KV RMWEAIETYM+RKQPLI+IAGADYGQGSSRDWAAKGVRLAG E IVAEGFERIHRTN
Sbjct: 716 KVTRMWEAIETYMERKQPLIVIAGADYGQGSSRDWAAKGVRLAGAEAIVAEGFERIHRTN 775
Query: 781 LIGMGVLPLEFKPGVNRLTLGLDGTETYDVIGERQPRATLTLVVNRKNGERVEVPVTCRL 840
L+GMGVLPLEFKPGVNRLTL +DGTET+DVIGER+PRA LTLV++RKNGERVEVPVTCRL
Sbjct: 776 LVGMGVLPLEFKPGVNRLTLAIDGTETFDVIGERKPRADLTLVIHRKNGERVEVPVTCRL 835
Query: 841 DSDEEVSIYEAGGVL-HFAQDFLESSRATA 869
D+ EEVSIYEAGGVL FAQDFLESS+ A
Sbjct: 836 DTAEEVSIYEAGGVLQRFAQDFLESSKKAA 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: 2239
Number of extensions: 85
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 BPHYT_RS30145 BPHYT_RS30145 (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.12323.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 1778.4 0.1 0 1778.2 0.1 1.0 1 lcl|FitnessBrowser__BFirm:BPHYT_RS30145 BPHYT_RS30145 aconitate hydratas
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__BFirm:BPHYT_RS30145 BPHYT_RS30145 aconitate hydratase
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1778.2 0.1 0 0 1 858 [] 2 859 .. 2 859 .. 1.00
Alignments for each domain:
== domain 1 score: 1778.2 bits; conditional E-value: 0
TIGR02333 1 ntkyrkalpgtdldyfdaraaveaikpgaydklpytsrvlaenlvrrvdpetleaslkqlierkreldfp 70
nt+ rk lpgt+ld+fd+raav+ai+pgaydklpytsrvlaenlvrr+dp tl+aslkq+ierkreldfp
lcl|FitnessBrowser__BFirm:BPHYT_RS30145 2 NTANRKRLPGTQLDFFDTRAAVDAIQPGAYDKLPYTSRVLAENLVRRCDPVTLTASLKQIIERKRELDFP 71
7899****************************************************************** PP
TIGR02333 71 wyparvvchdilgqtalvdlaglrdaiaekggdpaqvnpvvetqlivdhslaveyggfdpdafeknraie 140
w+parvvchdilgqtalvdlaglrdaia++ggdpa vnpvv+tql+vdhslave+ggfdpdaf+knraie
lcl|FitnessBrowser__BFirm:BPHYT_RS30145 72 WFPARVVCHDILGQTALVDLAGLRDAIAAQGGDPALVNPVVPTQLVVDHSLAVECGGFDPDAFAKNRAIE 141
********************************************************************** PP
TIGR02333 141 drrnedrfhfinwtkkafknvdvipagngimhqinlekmspvvqvkegvafpdtlvgtdshtphvdalgv 210
drrnedrf finwtk+af+nvdvip+gngi+hqinle+mspvvqvk+gvafpdtlvgtdshtp vdalgv
lcl|FitnessBrowser__BFirm:BPHYT_RS30145 142 DRRNEDRFDFINWTKRAFRNVDVIPPGNGILHQINLERMSPVVQVKDGVAFPDTLVGTDSHTPMVDALGV 211
********************************************************************** PP
TIGR02333 211 iaigvggleaetvmlgraslmrlpdivgveltgkrqpgitatdivlalteflrkekvvsayleffgegak 280
iaigvggleae+vmlgras+mrlpdivgveltgk + gitatd+vl+lteflrkekvv+aylef+g g+
lcl|FitnessBrowser__BFirm:BPHYT_RS30145 212 IAIGVGGLEAESVMLGRASYMRLPDIVGVELTGKPAEGITATDVVLSLTEFLRKEKVVGAYLEFYGTGTA 281
********************************************************************** PP
TIGR02333 281 altlgdratisnmtpeygataamfaideqtidylkltgreeeqvklvetyakaaglwadslkkavyervl 350
ltlgdrati+nm+pe+gataamf ideqti+ylkltgr++e vk vetyak +glwadsl +a+yervl
lcl|FitnessBrowser__BFirm:BPHYT_RS30145 282 KLTLGDRATIANMAPEFGATAAMFSIDEQTIKYLKLTGRDDELVKRVETYAKKTGLWADSLVNAEYERVL 351
********************************************************************** PP
TIGR02333 351 kfdlssvvrnlagpsnpharlatsdlaakgiakeveeeaeglmpdgaviiaaitsctntsnprnvvaagl 420
kfdls+vvr+lagpsnph+rl+ s+laa+gi+++ve+e+ glmpdgaviiaaitsctnt nprn++aagl
lcl|FitnessBrowser__BFirm:BPHYT_RS30145 352 KFDLSTVVRTLAGPSNPHRRLPVSELAARGISGKVENEP-GLMPDGAVIIAAITSCTNTNNPRNMIAAGL 420
***************************************.****************************** PP
TIGR02333 421 larnanklglkrkpwvksslapgskvvklyleeagllkeleklgfgivafacttcngmsgaldpviqqei 490
larnan++gl+rkpw k+slapgsk+v lyleeagll+ele+lgfg+va+act+cngmsgaldpviq+ei
lcl|FitnessBrowser__BFirm:BPHYT_RS30145 421 LARNANRRGLTRKPWAKTSLAPGSKAVTLYLEEAGLLPELEQLGFGVVAYACTSCNGMSGALDPVIQKEI 490
********************************************************************** PP
TIGR02333 491 idrdlyatavlsgnrnfdgrihpyakqaflaspplvvayaiagtirfdiekdvlgvdadgkeirlkdiwp 560
++rdlyatavlsgnrnfdgrihpyakqaflaspplvvayaiagtirfdiekdvlg+dadg+ + lkdiwp
lcl|FitnessBrowser__BFirm:BPHYT_RS30145 491 VERDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTIRFDIEKDVLGIDADGQAVTLKDIWP 560
********************************************************************** PP
TIGR02333 561 sdeeidavvaaavkpeqfrkvyipmfdle.daqkkvsplydwrpmstyirrppywegalagertlkgmrp 629
+d+eida+va++vkpeqfrkvy+pmf+++ d+++k+ ply+wrpmstyirrppywegalagertlkgmrp
lcl|FitnessBrowser__BFirm:BPHYT_RS30145 561 TDAEIDAIVASSVKPEQFRKVYEPMFAVSvDTGEKADPLYNWRPMSTYIRRPPYWEGALAGERTLKGMRP 630
********************************************************************** PP
TIGR02333 630 lavlgdnittdhlspsnailldsaageylakmglpeedfnsyathrgdhltaqratfanpklfnemvked 699
lavlgdnittdhlspsnail+dsa+geylakmglpeedfnsyathrgdhltaqratfanp l+nemv ed
lcl|FitnessBrowser__BFirm:BPHYT_RS30145 631 LAVLGDNITTDHLSPSNAILADSASGEYLAKMGLPEEDFNSYATHRGDHLTAQRATFANPTLKNEMVLED 700
********************************************************************** PP
TIGR02333 700 gkvkqgslariepegkvtrmweaietymnrkqpliiiagadygqgssrdwaakgvrlagveaivaegfer 769
gkvk gslariepegkvtrmweaietym+rkqpli+iagadygqgssrdwaakgvrlag eaivaegfer
lcl|FitnessBrowser__BFirm:BPHYT_RS30145 701 GKVKAGSLARIEPEGKVTRMWEAIETYMERKQPLIVIAGADYGQGSSRDWAAKGVRLAGAEAIVAEGFER 770
********************************************************************** PP
TIGR02333 770 ihrtnlvgmgvlplefkpgtnrktlaldgtevydvvgeitpradltlvvtrkngeklevpvtcrldtaee 839
ihrtnlvgmgvlplefkpg+nr tla+dgte++dv+ge++pradltlv++rknge++evpvtcrldtaee
lcl|FitnessBrowser__BFirm:BPHYT_RS30145 771 IHRTNLVGMGVLPLEFKPGVNRLTLAIDGTETFDVIGERKPRADLTLVIHRKNGERVEVPVTCRLDTAEE 840
********************************************************************** PP
TIGR02333 840 vsvyeaggvlqrfaqdfle 858
vs+yeaggvlqrfaqdfle
lcl|FitnessBrowser__BFirm:BPHYT_RS30145 841 VSIYEAGGVLQRFAQDFLE 859
*****************97 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 0.03s 00:00:00.09 Elapsed: 00:00:00.08
# Mc/sec: 9.21
//
[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