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 Pf1N1B4_3821 2-methylcitrate dehydratase FeS dependent (EC 4.2.1.79)
Query= SwissProt::Q937N8
(869 letters)
>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3821
Length = 864
Score = 1439 bits (3724), Expect = 0.0
Identities = 723/866 (83%), Positives = 780/866 (90%), Gaps = 7/866 (0%)
Query: 1 MNSANRKPLPGTKLDYFDARAAVEAIQPGAYDKLPYTSRVLAENLVRRCDPATLTDSLLQ 60
MN+ RKPLPG+ LDYFD RAAV+AI PGAYD LPYTSRVLAENLVRRCDPATLT+SL Q
Sbjct: 1 MNTEFRKPLPGSHLDYFDVRAAVDAISPGAYDTLPYTSRVLAENLVRRCDPATLTESLKQ 60
Query: 61 LVGRKRDLDFPWFPARVVCHDILGQTALVDLAGLRDAIADQGGDPAKVNPVVPVQLIVDH 120
+ RKRDLDFPWFPARVVCHDILGQTALVDLAGLRDAIA QGGDPA+VNPVVP QLIVDH
Sbjct: 61 FIERKRDLDFPWFPARVVCHDILGQTALVDLAGLRDAIALQGGDPAQVNPVVPTQLIVDH 120
Query: 121 SLAVECGGFDPDAFAKNRAIEDRRNEDRFHFIDWTKQAFKNVDVIPPGNGIMHQINLEKM 180
SLAVE GGFDP+AF KNRAIEDRRNEDRFHFI+WTK+AFKNVDVIPPGNGIMHQINLEKM
Sbjct: 121 SLAVERGGFDPEAFEKNRAIEDRRNEDRFHFINWTKKAFKNVDVIPPGNGIMHQINLEKM 180
Query: 181 SPVIHADNGVAYPDTCVGTDSHTPHVDALGVIAIGVGGLEAENVMLGRASWMRLPDIVGV 240
SPVI +GVA+PDTCVGTDSHTPHVDALGVIAIGVGGLEAE+VMLGRASWMRLP+ VGV
Sbjct: 181 SPVIQVRDGVAFPDTCVGTDSHTPHVDALGVIAIGVGGLEAESVMLGRASWMRLPESVGV 240
Query: 241 ELTGKRQPGITATDIVLALTEFLRKEKVVGAYLEFRGEGASSLTLGDRATISNMAPEYGA 300
ELTGK QPGITATD+VLALTE+LRK+KVVGA+LEF GEGAS+LTLGDRATISNMAPEYGA
Sbjct: 241 ELTGKLQPGITATDMVLALTEYLRKQKVVGAWLEFFGEGASALTLGDRATISNMAPEYGA 300
Query: 301 TAAMFFIDEQTIDYLRLTGRTDEQLKLVETYARTAGLWADSLKNAEYERVLKFDLSSVVR 360
TAAMF+ID+QTIDYL+LTGR DEQ++LVE+YA+ GLWADSLK A+YER L FDLSSVVR
Sbjct: 301 TAAMFYIDQQTIDYLKLTGREDEQVQLVESYAKQTGLWADSLKGAQYERGLTFDLSSVVR 360
Query: 361 NMAGPSNPHKRLPTSALAERGIAVDLDKASAQEAEGLMPDGAVIIAAITSCTNTSNPRNV 420
NMAGPSNPH R+ S LA +GI+ D + G MPDGAVIIAAITSCTNTSNPRNV
Sbjct: 361 NMAGPSNPHARVAVSDLAAKGISGQWD-----DVPGQMPDGAVIIAAITSCTNTSNPRNV 415
Query: 421 IAAALLARNANARGLARKPWVKSSLAPGSKAVELYLEEANLLPDLEKLGFGIVAFACTTC 480
IAA LLARNAN GL RKPWVKSSLAPGSK V LYL+EA L +LE+LGFG+VAFACTTC
Sbjct: 416 IAAGLLARNANKLGLTRKPWVKSSLAPGSKTVALYLDEAGLTSELEQLGFGVVAFACTTC 475
Query: 481 NGMSGALDPKIQQEIIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTI 540
NGMSGALDP IQQEIIDRDLYATAVLSGNRNFDGRIHPYAK AFLASPPLVVAYAIAGTI
Sbjct: 476 NGMSGALDPVIQQEIIDRDLYATAVLSGNRNFDGRIHPYAKNAFLASPPLVVAYAIAGTI 535
Query: 541 RFDIEKDVLGTDQDGKPVYLKDIWPSDEEIDAIVAKSVKPEQFRKVYEPMFAITAASGES 600
RFDIEKDVLG DGK + LKDIWPSDEEIDA+V SVKPEQFR+VY PMFAI +G
Sbjct: 536 RFDIEKDVLGV-VDGKEIRLKDIWPSDEEIDAVVKASVKPEQFRQVYIPMFAIHEDTGPK 594
Query: 601 VSPLYDWRPQSTYIRRPPYWEGALAGERTLKALRPLAVLGDNITTDHLSPSNAIMLNSAA 660
V+PLYDWR STYIRRPPYWEGALAG R LK +RPLAVL DNITTDHLSPSNAIML+SAA
Sbjct: 595 VAPLYDWREMSTYIRRPPYWEGALAGARPLKGMRPLAVLPDNITTDHLSPSNAIMLDSAA 654
Query: 661 GEYLARMGLPEEDFNSYATHRGDHLTAQRATFANPTLINEMAVVDGQVKKGSLARIEPEG 720
GEYLA+MGLPEEDFNSYATHRGDHLTAQRATFANP L NEM +G+VK+GSLAR+EPEG
Sbjct: 655 GEYLAKMGLPEEDFNSYATHRGDHLTAQRATFANPKLFNEMVQENGKVKQGSLARVEPEG 714
Query: 721 KVVRMWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEVIVAEGFERIHRTN 780
+V+RMWEAIETYM+RKQPLIIIAGADYGQGSSRDWAAKGVRLAGVE I AEGFERIHRTN
Sbjct: 715 QVMRMWEAIETYMERKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEAIAAEGFERIHRTN 774
Query: 781 LIGMGVLPLEFKPGVNRLTLGLDGTETYDVIGERQPRATLTLVVNRKNGERVEVPVTCRL 840
L+GMGVLPLEF+PG +R TL +DG+ETYDVIG+R PRATLTLV+NRKNGERVEVPVTCRL
Sbjct: 775 LVGMGVLPLEFQPGTDRHTLAIDGSETYDVIGDRTPRATLTLVINRKNGERVEVPVTCRL 834
Query: 841 DSDEEVSIYEAGGVL-HFAQDFLESS 865
D+ EEVSIYEAGGVL FAQDFLE S
Sbjct: 835 DTAEEVSIYEAGGVLQRFAQDFLEES 860
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: 2217
Number of extensions: 81
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: 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 Pf1N1B4_3821 (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.27722.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 1828.6 0.0 0 1828.4 0.0 1.0 1 lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3821 2-methylcitrate dehydratase FeS
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3821 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 ! 1828.4 0.0 0 0 1 858 [] 2 858 .. 2 858 .. 1.00
Alignments for each domain:
== domain 1 score: 1828.4 bits; conditional E-value: 0
TIGR02333 1 ntkyrkalpgtdldyfdaraaveaikpgaydklpytsrvlaenlvrrvdpetleaslkqlierk 64
nt++rk+lpg++ldyfd raav+ai pgayd+lpytsrvlaenlvrr+dp+tl++slkq+ierk
lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3821 2 NTEFRKPLPGSHLDYFDVRAAVDAISPGAYDTLPYTSRVLAENLVRRCDPATLTESLKQFIERK 65
899************************************************************* PP
TIGR02333 65 reldfpwyparvvchdilgqtalvdlaglrdaiaekggdpaqvnpvvetqlivdhslaveyggf 128
r+ldfpw+parvvchdilgqtalvdlaglrdaia +ggdpaqvnpvv+tqlivdhslave ggf
lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3821 66 RDLDFPWFPARVVCHDILGQTALVDLAGLRDAIALQGGDPAQVNPVVPTQLIVDHSLAVERGGF 129
**************************************************************** PP
TIGR02333 129 dpdafeknraiedrrnedrfhfinwtkkafknvdvipagngimhqinlekmspvvqvkegvafp 192
dp+afeknraiedrrnedrfhfinwtkkafknvdvip+gngimhqinlekmspv+qv++gvafp
lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3821 130 DPEAFEKNRAIEDRRNEDRFHFINWTKKAFKNVDVIPPGNGIMHQINLEKMSPVIQVRDGVAFP 193
**************************************************************** PP
TIGR02333 193 dtlvgtdshtphvdalgviaigvggleaetvmlgraslmrlpdivgveltgkrqpgitatdivl 256
dt+vgtdshtphvdalgviaigvggleae+vmlgras+mrlp+ vgveltgk qpgitatd+vl
lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3821 194 DTCVGTDSHTPHVDALGVIAIGVGGLEAESVMLGRASWMRLPESVGVELTGKLQPGITATDMVL 257
**************************************************************** PP
TIGR02333 257 alteflrkekvvsayleffgegakaltlgdratisnmtpeygataamfaideqtidylkltgre 320
alte+lrk+kvv+a+leffgega altlgdratisnm+peygataamf+id+qtidylkltgre
lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3821 258 ALTEYLRKQKVVGAWLEFFGEGASALTLGDRATISNMAPEYGATAAMFYIDQQTIDYLKLTGRE 321
**************************************************************** PP
TIGR02333 321 eeqvklvetyakaaglwadslkkavyervlkfdlssvvrnlagpsnpharlatsdlaakgiake 384
+eqv+lve+yak +glwadslk a+yer l+fdlssvvrn+agpsnphar+a sdlaakgi+++
lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3821 322 DEQVQLVESYAKQTGLWADSLKGAQYERGLTFDLSSVVRNMAGPSNPHARVAVSDLAAKGISGQ 385
**************************************************************** PP
TIGR02333 385 veeeaeglmpdgaviiaaitsctntsnprnvvaagllarnanklglkrkpwvksslapgskvvk 448
+++++ g+mpdgaviiaaitsctntsnprnv+aagllarnanklgl+rkpwvksslapgsk+v
lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3821 386 WDDVP-GQMPDGAVIIAAITSCTNTSNPRNVIAAGLLARNANKLGLTRKPWVKSSLAPGSKTVA 448
*****.********************************************************** PP
TIGR02333 449 lyleeagllkeleklgfgivafacttcngmsgaldpviqqeiidrdlyatavlsgnrnfdgrih 512
lyl+eagl +ele+lgfg+vafacttcngmsgaldpviqqeiidrdlyatavlsgnrnfdgrih
lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3821 449 LYLDEAGLTSELEQLGFGVVAFACTTCNGMSGALDPVIQQEIIDRDLYATAVLSGNRNFDGRIH 512
**************************************************************** PP
TIGR02333 513 pyakqaflaspplvvayaiagtirfdiekdvlgvdadgkeirlkdiwpsdeeidavvaaavkpe 576
pyak+aflaspplvvayaiagtirfdiekdvlgv +dgkeirlkdiwpsdeeidavv+a+vkpe
lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3821 513 PYAKNAFLASPPLVVAYAIAGTIRFDIEKDVLGV-VDGKEIRLKDIWPSDEEIDAVVKASVKPE 575
**********************************.***************************** PP
TIGR02333 577 qfrkvyipmfdle.daqkkvsplydwrpmstyirrppywegalagertlkgmrplavlgdnitt 639
qfr+vyipmf+++ d++ kv+plydwr mstyirrppywegalag r lkgmrplavl+dnitt
lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3821 576 QFRQVYIPMFAIHeDTGPKVAPLYDWREMSTYIRRPPYWEGALAGARPLKGMRPLAVLPDNITT 639
************989************************************************* PP
TIGR02333 640 dhlspsnailldsaageylakmglpeedfnsyathrgdhltaqratfanpklfnemvkedgkvk 703
dhlspsnai+ldsaageylakmglpeedfnsyathrgdhltaqratfanpklfnemv+e+gkvk
lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3821 640 DHLSPSNAIMLDSAAGEYLAKMGLPEEDFNSYATHRGDHLTAQRATFANPKLFNEMVQENGKVK 703
**************************************************************** PP
TIGR02333 704 qgslariepegkvtrmweaietymnrkqpliiiagadygqgssrdwaakgvrlagveaivaegf 767
qgslar+epeg+v+rmweaietym+rkqpliiiagadygqgssrdwaakgvrlagveai aegf
lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3821 704 QGSLARVEPEGQVMRMWEAIETYMERKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEAIAAEGF 767
**************************************************************** PP
TIGR02333 768 erihrtnlvgmgvlplefkpgtnrktlaldgtevydvvgeitpradltlvvtrkngeklevpvt 831
erihrtnlvgmgvlplef+pgt+r+tla+dg+e+ydv+g++tpra+ltlv++rknge++evpvt
lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3821 768 ERIHRTNLVGMGVLPLEFQPGTDRHTLAIDGSETYDVIGDRTPRATLTLVINRKNGERVEVPVT 831
**************************************************************** PP
TIGR02333 832 crldtaeevsvyeaggvlqrfaqdfle 858
crldtaeevs+yeaggvlqrfaqdfle
lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3821 832 CRLDTAEEVSIYEAGGVLQRFAQDFLE 858
*************************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: 00:00:00.07
# Mc/sec: 10.46
//
[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