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 Ac3H11_2323 2-methylcitrate dehydratase FeS dependent (EC 4.2.1.79)
Query= SwissProt::Q937N8
(869 letters)
>FitnessBrowser__acidovorax_3H11:Ac3H11_2323
Length = 889
Score = 1391 bits (3601), Expect = 0.0
Identities = 705/875 (80%), Positives = 771/875 (88%), Gaps = 9/875 (1%)
Query: 1 MNSANRKPLPGTKLDYFDARAAVEAIQPGAYDKLPYTSRVLAENLVRRCDPATLTDSLLQ 60
MN+ R+PLPGT LDYFDARAAVE +QPGA+ LPYT+RV AE++VRR DPAT+ D L Q
Sbjct: 2 MNTLFRRPLPGTDLDYFDARAAVETLQPGAWATLPYTARVHAESIVRRADPATVNDCLRQ 61
Query: 61 LVGRKRDLDFPWFPARVVCHDILGQTALVDLAGLRDAIADQGGDPAKVNPVVPVQLIVDH 120
L+ RKRD DFPW+PARVVCHDILGQTALVDLAGLRDAIA GGDPA+VNPVVPVQLIVDH
Sbjct: 62 LIERKRDRDFPWYPARVVCHDILGQTALVDLAGLRDAIAKGGGDPAQVNPVVPVQLIVDH 121
Query: 121 SLAVECGGFDPDAFAKNRAIEDRRNEDRFHFIDWTKQAFKNVDVIPPGNGIMHQINLEKM 180
SLAVECGGFDPDAFAKNRAIEDRRNEDRFHFI+WTK+AF NVDVIP GNGIMHQINLEKM
Sbjct: 122 SLAVECGGFDPDAFAKNRAIEDRRNEDRFHFIEWTKKAFANVDVIPAGNGIMHQINLEKM 181
Query: 181 SPVIHADNGVAYPDTCVGTDSHTPHVDALGVIAIGVGGLEAENVMLGRASWMRLPDIVGV 240
SPV+HAD GVAYPDTCVGTDSHTPHVDALGVIAIGVGGLEAENVMLGRAS MRLP++VGV
Sbjct: 182 SPVVHADRGVAYPDTCVGTDSHTPHVDALGVIAIGVGGLEAENVMLGRASMMRLPEMVGV 241
Query: 241 ELTGKRQPGITATDIVLALTEFLRKEKVVGAYLEFRGEGASSLTLGDRATISNMAPEYGA 300
ELTG+RQ GITATD+VLALTEFLRK KVVGAYLEF GEGA+ LTLGDRATISNMAPEYGA
Sbjct: 242 ELTGQRQDGITATDVVLALTEFLRKAKVVGAYLEFFGEGAAKLTLGDRATISNMAPEYGA 301
Query: 301 TAAMFFIDEQTIDYLRLTGRTDEQLKLVETYARTAGLWADSLKNAEYERVLKFDLSSVVR 360
TAA+F IDEQT+DYLRLTGR Q+KLVETYA+TAGLWAD+L A Y+R L+FDLS+VVR
Sbjct: 302 TAALFCIDEQTLDYLRLTGREARQVKLVETYAKTAGLWADALAGAVYDRTLRFDLSTVVR 361
Query: 361 NMAGPSNPHKRLPTSALAERGIAVDLDKASAQEAEGLMPDGAVIIAAITSCTNTSNPRNV 420
N+AGPSNPH R+ TS LA RGIA A EG MPDGAV+IAAITSCTNTSNPRNV
Sbjct: 362 NLAGPSNPHARVATSDLAARGIAGPW--ALPSPGEGTMPDGAVVIAAITSCTNTSNPRNV 419
Query: 421 IAAALLARNANARGLARKPWVKSSLAPGSKAVELYLEEANLLPDLEKLGFGIVAFACTTC 480
IAAALLARNA+ GL RKPWVK+SLAPGS+ VELYL+EA LL DLE LGFGIVAFACTTC
Sbjct: 420 IAAALLARNAHRLGLTRKPWVKTSLAPGSRVVELYLKEAGLLTDLEALGFGIVAFACTTC 479
Query: 481 NGMSGALDPKIQQEIIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTI 540
NGMSGALDP IQQEIIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGT+
Sbjct: 480 NGMSGALDPAIQQEIIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTV 539
Query: 541 RFDIEKDVLGTDQDGKPVYLKDIWPSDEEIDAIVAKSVKPEQFRKVYEPMFAITAASGES 600
RFDIEKDVL DG+P+ LKD+WPSDEEIDA+V +VKP +R VYEPMFAI G
Sbjct: 540 RFDIEKDVLAV-VDGQPIRLKDLWPSDEEIDAVVKAAVKPAHYRAVYEPMFAIRHDDGPR 598
Query: 601 VSPLYDWRPQSTYIRRPPYWE----GALAGE-RTLKALRPLAVLGDNITTDHLSPSNAIM 655
VSP YDWRPQSTYIRRPPYW+ GALA RTL+ +RPLA+L DNITTDHLSPSNAI+
Sbjct: 599 VSPQYDWRPQSTYIRRPPYWDTEGIGALAAHPRTLQGMRPLALLPDNITTDHLSPSNAIL 658
Query: 656 LNSAAGEYLARMGLPEEDFNSYATHRGDHLTAQRATFANPTLINEMAVVDGQVKKGSLAR 715
+SAAGEYLARMGLPEEDFNSYATHRGDHLTA RATFANP L+NEMAVVDG+V+KGSLAR
Sbjct: 659 PDSAAGEYLARMGLPEEDFNSYATHRGDHLTALRATFANPQLVNEMAVVDGKVQKGSLAR 718
Query: 716 IEPEGKVVRMWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEVIVAEGFER 775
+EPEG+V+RMWEAIETY+ R+QPLIIIAGADYGQGSSRDWAAKGVRLAGVEV+VAEGFER
Sbjct: 719 VEPEGQVMRMWEAIETYLHRRQPLIIIAGADYGQGSSRDWAAKGVRLAGVEVVVAEGFER 778
Query: 776 IHRTNLIGMGVLPLEFKPGVNRLTLGLDGTETYDVIGERQPRATLTLVVNRKNGERVEVP 835
IHRTNLIGMGVLPLEF+ GVNR TL L+GTE Y V G+ +P AT+TLVV RK GE V+VP
Sbjct: 779 IHRTNLIGMGVLPLEFEAGVNRTTLQLEGTEVYGVEGDLKPGATVTLVVQRKLGEVVKVP 838
Query: 836 VTCRLDSDEEVSIYEAGGVL-HFAQDFLESSRATA 869
+ CRLD+ EEVS+YEAGGVL FAQDFL + A
Sbjct: 839 MRCRLDTAEEVSVYEAGGVLQRFAQDFLAARAGAA 873
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: 2236
Number of extensions: 92
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: 889
Length adjustment: 43
Effective length of query: 826
Effective length of database: 846
Effective search space: 698796
Effective search space used: 698796
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 Ac3H11_2323 (2-methylcitrate dehydratase FeS dependent (EC 4.2.1.79))
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.1223.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 1710.6 0.2 0 1710.5 0.2 1.0 1 lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2323 2-methylcitrate dehydratase FeS
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2323 2-methylcitrate dehydratase FeS dependent (EC 4.2.1.79)
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1710.5 0.2 0 0 1 858 [] 3 867 .. 3 867 .. 0.99
Alignments for each domain:
== domain 1 score: 1710.5 bits; conditional E-value: 0
TIGR02333 1 ntkyrkalpgtdldyfdaraaveaikpgaydklpytsrvlaenlvrrvdpetleaslkqlie 62
nt +r++lpgtdldyfdaraave+++pga+++lpyt+rv ae +vrr+dp+t+++ l+qlie
lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2323 3 NTLFRRPLPGTDLDYFDARAAVETLQPGAWATLPYTARVHAESIVRRADPATVNDCLRQLIE 64
799*********************************************************** PP
TIGR02333 63 rkreldfpwyparvvchdilgqtalvdlaglrdaiaekggdpaqvnpvvetqlivdhslave 124
rkr+ dfpwyparvvchdilgqtalvdlaglrdaia+ ggdpaqvnpvv++qlivdhslave
lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2323 65 RKRDRDFPWYPARVVCHDILGQTALVDLAGLRDAIAKGGGDPAQVNPVVPVQLIVDHSLAVE 126
************************************************************** PP
TIGR02333 125 yggfdpdafeknraiedrrnedrfhfinwtkkafknvdvipagngimhqinlekmspvvqvk 186
+ggfdpdaf+knraiedrrnedrfhfi+wtkkaf nvdvipagngimhqinlekmspvv+++
lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2323 127 CGGFDPDAFAKNRAIEDRRNEDRFHFIEWTKKAFANVDVIPAGNGIMHQINLEKMSPVVHAD 188
************************************************************** PP
TIGR02333 187 egvafpdtlvgtdshtphvdalgviaigvggleaetvmlgraslmrlpdivgveltgkrqpg 248
+gva+pdt+vgtdshtphvdalgviaigvggleae+vmlgras+mrlp++vgveltg+rq g
lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2323 189 RGVAYPDTCVGTDSHTPHVDALGVIAIGVGGLEAENVMLGRASMMRLPEMVGVELTGQRQDG 250
************************************************************** PP
TIGR02333 249 itatdivlalteflrkekvvsayleffgegakaltlgdratisnmtpeygataamfaideqt 310
itatd+vlalteflrk kvv+ayleffgega ltlgdratisnm+peygataa+f ideqt
lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2323 251 ITATDVVLALTEFLRKAKVVGAYLEFFGEGAAKLTLGDRATISNMAPEYGATAALFCIDEQT 312
************************************************************** PP
TIGR02333 311 idylkltgreeeqvklvetyakaaglwadslkkavyervlkfdlssvvrnlagpsnpharla 372
+dyl+ltgre++qvklvetyak+aglwad+l avy+r+l+fdls+vvrnlagpsnphar+a
lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2323 313 LDYLRLTGREARQVKLVETYAKTAGLWADALAGAVYDRTLRFDLSTVVRNLAGPSNPHARVA 374
************************************************************** PP
TIGR02333 373 tsdlaakgiakevee..eaeglmpdgaviiaaitsctntsnprnvvaagllarnanklglkr 432
tsdlaa+gia+++ eg mpdgav+iaaitsctntsnprnv+aa+llarna +lgl+r
lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2323 375 TSDLAARGIAGPWALpsPGEGTMPDGAVVIAAITSCTNTSNPRNVIAAALLARNAHRLGLTR 436
************986336799***************************************** PP
TIGR02333 433 kpwvksslapgskvvklyleeagllkeleklgfgivafacttcngmsgaldpviqqeiidrd 494
kpwvk+slapgs+vv+lyl+eagll++le lgfgivafacttcngmsgaldp+iqqeiidrd
lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2323 437 KPWVKTSLAPGSRVVELYLKEAGLLTDLEALGFGIVAFACTTCNGMSGALDPAIQQEIIDRD 498
************************************************************** PP
TIGR02333 495 lyatavlsgnrnfdgrihpyakqaflaspplvvayaiagtirfdiekdvlgvdadgkeirlk 556
lyatavlsgnrnfdgrihpyakqaflaspplvvayaiagt+rfdiekdvl v +dg++irlk
lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2323 499 LYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTVRFDIEKDVLAV-VDGQPIRLK 559
****************************************************.********* PP
TIGR02333 557 diwpsdeeidavvaaavkpeqfrkvyipmfdle.daqkkvsplydwrpmstyirrppywe.. 615
d+wpsdeeidavv+aavkp +r vy+pmf++ d + +vsp ydwrp+styirrppyw+
lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2323 560 DLWPSDEEIDAVVKAAVKPAHYRAVYEPMFAIRhDDGPRVSPQYDWRPQSTYIRRPPYWDte 621
********************************9899***********************766 PP
TIGR02333 616 ..galag.ertlkgmrplavlgdnittdhlspsnailldsaageylakmglpeedfnsyath 674
gala+ +rtl+gmrpla+l+dnittdhlspsnail dsaageyla+mglpeedfnsyath
lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2323 622 giGALAAhPRTLQGMRPLALLPDNITTDHLSPSNAILPDSAAGEYLARMGLPEEDFNSYATH 683
668998747***************************************************** PP
TIGR02333 675 rgdhltaqratfanpklfnemvkedgkvkqgslariepegkvtrmweaietymnrkqpliii 736
rgdhlta ratfanp+l+nem+ +dgkv++gslar+epeg+v+rmweaiety++r+qpliii
lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2323 684 RGDHLTALRATFANPQLVNEMAVVDGKVQKGSLARVEPEGQVMRMWEAIETYLHRRQPLIII 745
************************************************************** PP
TIGR02333 737 agadygqgssrdwaakgvrlagveaivaegferihrtnlvgmgvlplefkpgtnrktlaldg 798
agadygqgssrdwaakgvrlagve +vaegferihrtnl+gmgvlplef +g+nr+tl+l+g
lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2323 746 AGADYGQGSSRDWAAKGVRLAGVEVVVAEGFERIHRTNLIGMGVLPLEFEAGVNRTTLQLEG 807
************************************************************** PP
TIGR02333 799 tevydvvgeitpradltlvvtrkngeklevpvtcrldtaeevsvyeaggvlqrfaqdfle 858
tevy v g+ +p+a++tlvv+rk ge ++vp+ crldtaeevsvyeaggvlqrfaqdfl+
lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2323 808 TEVYGVEGDLKPGATVTLVVQRKLGEVVKVPMRCRLDTAEEVSVYEAGGVLQRFAQDFLA 867
**********************************************************95 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (858 nodes)
Target sequences: 1 (889 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: 00:00:00.09
# Mc/sec: 8.15
//
[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