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 PfGW456L13_4116 2-methylcitrate dehydratase FeS dependent (EC 4.2.1.79)
Query= SwissProt::Q937N8
(869 letters)
>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4116
Length = 864
Score = 1444 bits (3738), Expect = 0.0
Identities = 726/866 (83%), Positives = 781/866 (90%), Gaps = 7/866 (0%)
Query: 1 MNSANRKPLPGTKLDYFDARAAVEAIQPGAYDKLPYTSRVLAENLVRRCDPATLTDSLLQ 60
MN+ RKPLPG+ LDYFD RAAVEAIQPGAYD LPYTSRVLAENLVRRCDPATLT+SL Q
Sbjct: 1 MNTQFRKPLPGSHLDYFDVRAAVEAIQPGAYDTLPYTSRVLAENLVRRCDPATLTESLKQ 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+VLALTEFLRK+KVVGA+LEF GEGA++LTLGDRATISNMAPEYGA
Sbjct: 241 ELTGKLQPGITATDMVLALTEFLRKQKVVGAWLEFFGEGAAALTLGDRATISNMAPEYGA 300
Query: 301 TAAMFFIDEQTIDYLRLTGRTDEQLKLVETYARTAGLWADSLKNAEYERVLKFDLSSVVR 360
TAAMF+ID+QTIDYL+LTGR DEQ++LVE YA+ GLWADSLK A+YER L FDLSSVVR
Sbjct: 301 TAAMFYIDQQTIDYLKLTGREDEQVQLVENYAKQVGLWADSLKGAQYERGLTFDLSSVVR 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 IAAGLLARNANKLGLTRKPWVKSSLAPGSKTVALYLDEAGLTDELEQLGFGVVAFACTTC 475
Query: 481 NGMSGALDPKIQQEIIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTI 540
NGMSGALDP IQQEIIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTI
Sbjct: 476 NGMSGALDPVIQQEIIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTI 535
Query: 541 RFDIEKDVLGTDQDGKPVYLKDIWPSDEEIDAIVAKSVKPEQFRKVYEPMFAITAASGES 600
RFDIEKDVLG DGK + LKDIWPSDEEIDA+V SVKPEQFR+VY PMFAI +G
Sbjct: 536 RFDIEKDVLGV-VDGKEIRLKDIWPSDEEIDAVVKASVKPEQFRQVYIPMFAIHEDTGPK 594
Query: 601 VSPLYDWRPQSTYIRRPPYWEGALAGERTLKALRPLAVLGDNITTDHLSPSNAIMLNSAA 660
V+PLY+WR STYIRRPPYWEGALAG R LK +RPLAVL DNITTDHLSPSNAIML+SAA
Sbjct: 595 VAPLYEWREMSTYIRRPPYWEGALAGARPLKGMRPLAVLPDNITTDHLSPSNAIMLDSAA 654
Query: 661 GEYLARMGLPEEDFNSYATHRGDHLTAQRATFANPTLINEMAVVDGQVKKGSLARIEPEG 720
GEYLA+MGLPEEDFNSYATHRGDHLTAQRATFANP L NEM + +G+VK+GSLAR+EPEG
Sbjct: 655 GEYLAKMGLPEEDFNSYATHRGDHLTAQRATFANPKLFNEMVLENGKVKQGSLARVEPEG 714
Query: 721 KVVRMWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEVIVAEGFERIHRTN 780
KV+RMWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVE I AEGFERIHRTN
Sbjct: 715 KVMRMWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEAIAAEGFERIHRTN 774
Query: 781 LIGMGVLPLEFKPGVNRLTLGLDGTETYDVIGERQPRATLTLVVNRKNGERVEVPVTCRL 840
L+GMGVLPLEFKPG NR TL +DG+ETYDVIG+R PRA LTLV++RKNGERV+VPVTCRL
Sbjct: 775 LVGMGVLPLEFKPGTNRHTLAIDGSETYDVIGDRTPRAELTLVIHRKNGERVDVPVTCRL 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: 2219
Number of extensions: 87
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 PfGW456L13_4116 (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.2325.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 1834.3 0.0 0 1834.1 0.0 1.0 1 lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4116 2-methylcitrate dehydratase FeS
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4116 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 ! 1834.1 0.0 0 0 1 858 [] 2 858 .. 2 858 .. 1.00
Alignments for each domain:
== domain 1 score: 1834.1 bits; conditional E-value: 0
TIGR02333 1 ntkyrkalpgtdldyfdaraaveaikpgaydklpytsrvlaenlvrrvdpetlea 55
nt++rk+lpg++ldyfd raaveai+pgayd+lpytsrvlaenlvrr+dp+tl++
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4116 2 NTQFRKPLPGSHLDYFDVRAAVEAIQPGAYDTLPYTSRVLAENLVRRCDPATLTE 56
89***************************************************** PP
TIGR02333 56 slkqlierkreldfpwyparvvchdilgqtalvdlaglrdaiaekggdpaqvnpv 110
slkq+ierkr+ldfpw+parvvchdilgqtalvdlaglrdaia +ggdpaqvnpv
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4116 57 SLKQFIERKRDLDFPWFPARVVCHDILGQTALVDLAGLRDAIALQGGDPAQVNPV 111
******************************************************* PP
TIGR02333 111 vetqlivdhslaveyggfdpdafeknraiedrrnedrfhfinwtkkafknvdvip 165
v+tqlivdhslave ggfdp+afeknraiedrrnedrfhfinwtkkafknvdvip
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4116 112 VPTQLIVDHSLAVERGGFDPEAFEKNRAIEDRRNEDRFHFINWTKKAFKNVDVIP 166
******************************************************* PP
TIGR02333 166 agngimhqinlekmspvvqvkegvafpdtlvgtdshtphvdalgviaigvgglea 220
+gngimhqinlekmspv+qv++gvafpdt+vgtdshtphvdalgviaigvgglea
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4116 167 PGNGIMHQINLEKMSPVIQVRDGVAFPDTCVGTDSHTPHVDALGVIAIGVGGLEA 221
******************************************************* PP
TIGR02333 221 etvmlgraslmrlpdivgveltgkrqpgitatdivlalteflrkekvvsayleff 275
e+vmlgras+mrlp+ vgveltgk qpgitatd+vlalteflrk+kvv+a+leff
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4116 222 ESVMLGRASWMRLPESVGVELTGKLQPGITATDMVLALTEFLRKQKVVGAWLEFF 276
******************************************************* PP
TIGR02333 276 gegakaltlgdratisnmtpeygataamfaideqtidylkltgreeeqvklvety 330
gega altlgdratisnm+peygataamf+id+qtidylkltgre+eqv+lve y
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4116 277 GEGAAALTLGDRATISNMAPEYGATAAMFYIDQQTIDYLKLTGREDEQVQLVENY 331
******************************************************* PP
TIGR02333 331 akaaglwadslkkavyervlkfdlssvvrnlagpsnpharlatsdlaakgiakev 385
ak glwadslk a+yer l+fdlssvvrn+agpsnphar+a sdlaakgi++++
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4116 332 AKQVGLWADSLKGAQYERGLTFDLSSVVRNMAGPSNPHARVAVSDLAAKGISGQW 386
******************************************************* PP
TIGR02333 386 eeeaeglmpdgaviiaaitsctntsnprnvvaagllarnanklglkrkpwvkssl 440
++++ g+mpdgaviiaaitsctntsnprnv+aagllarnanklgl+rkpwvkssl
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4116 387 DDVP-GQMPDGAVIIAAITSCTNTSNPRNVIAAGLLARNANKLGLTRKPWVKSSL 440
****.************************************************** PP
TIGR02333 441 apgskvvklyleeagllkeleklgfgivafacttcngmsgaldpviqqeiidrdl 495
apgsk+v lyl+eagl +ele+lgfg+vafacttcngmsgaldpviqqeiidrdl
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4116 441 APGSKTVALYLDEAGLTDELEQLGFGVVAFACTTCNGMSGALDPVIQQEIIDRDL 495
******************************************************* PP
TIGR02333 496 yatavlsgnrnfdgrihpyakqaflaspplvvayaiagtirfdiekdvlgvdadg 550
yatavlsgnrnfdgrihpyakqaflaspplvvayaiagtirfdiekdvlgv +dg
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4116 496 YATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTIRFDIEKDVLGV-VDG 549
***************************************************.*** PP
TIGR02333 551 keirlkdiwpsdeeidavvaaavkpeqfrkvyipmfdle.daqkkvsplydwrpm 604
keirlkdiwpsdeeidavv+a+vkpeqfr+vyipmf+++ d++ kv+ply+wr m
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4116 550 KEIRLKDIWPSDEEIDAVVKASVKPEQFRQVYIPMFAIHeDTGPKVAPLYEWREM 604
**************************************989************** PP
TIGR02333 605 styirrppywegalagertlkgmrplavlgdnittdhlspsnailldsaageyla 659
styirrppywegalag r lkgmrplavl+dnittdhlspsnai+ldsaageyla
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4116 605 STYIRRPPYWEGALAGARPLKGMRPLAVLPDNITTDHLSPSNAIMLDSAAGEYLA 659
******************************************************* PP
TIGR02333 660 kmglpeedfnsyathrgdhltaqratfanpklfnemvkedgkvkqgslariepeg 714
kmglpeedfnsyathrgdhltaqratfanpklfnemv e+gkvkqgslar+epeg
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4116 660 KMGLPEEDFNSYATHRGDHLTAQRATFANPKLFNEMVLENGKVKQGSLARVEPEG 714
******************************************************* PP
TIGR02333 715 kvtrmweaietymnrkqpliiiagadygqgssrdwaakgvrlagveaivaegfer 769
kv+rmweaietym+rkqpliiiagadygqgssrdwaakgvrlagveai aegfer
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4116 715 KVMRMWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEAIAAEGFER 769
******************************************************* PP
TIGR02333 770 ihrtnlvgmgvlplefkpgtnrktlaldgtevydvvgeitpradltlvvtrknge 824
ihrtnlvgmgvlplefkpgtnr+tla+dg+e+ydv+g++tpra+ltlv++rknge
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4116 770 IHRTNLVGMGVLPLEFKPGTNRHTLAIDGSETYDVIGDRTPRAELTLVIHRKNGE 824
******************************************************* PP
TIGR02333 825 klevpvtcrldtaeevsvyeaggvlqrfaqdfle 858
+++vpvtcrldtaeevs+yeaggvlqrfaqdfle
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4116 825 RVDVPVTCRLDTAEEVSIYEAGGVLQRFAQDFLE 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: 0.06u 0.03s 00:00:00.09 Elapsed: 00:00:00.08
# Mc/sec: 8.73
//
[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