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.23667.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: 0.07u 0.02s 00:00:00.09 Elapsed: 00:00:00.08
# Mc/sec: 9.01
//
[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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.
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