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 AO356_20875 AO356_20875 Fe/S-dependent 2-methylisocitrate dehydratase AcnD
Query= SwissProt::Q937N8
(869 letters)
>FitnessBrowser__pseudo5_N2C3_1:AO356_20875
Length = 863
Score = 1451 bits (3757), Expect = 0.0
Identities = 732/868 (84%), Positives = 783/868 (90%), Gaps = 7/868 (0%)
Query: 1 MNSANRKPLPGTKLDYFDARAAVEAIQPGAYDKLPYTSRVLAENLVRRCDPATLTDSLLQ 60
MN+ RKPLPGT LDYFD R AV+AI+PGAYD LPYTSRVLAENLVRRCDPATL +SLLQ
Sbjct: 1 MNTEFRKPLPGTSLDYFDVRGAVDAIRPGAYDGLPYTSRVLAENLVRRCDPATLRESLLQ 60
Query: 61 LVGRKRDLDFPWFPARVVCHDILGQTALVDLAGLRDAIADQGGDPAKVNPVVPVQLIVDH 120
L+ RKRDLDFPWFPARVVCHDILGQTALVDLAGLRDAIA QGGDPA+VNPVVP QLIVDH
Sbjct: 61 LIERKRDLDFPWFPARVVCHDILGQTALVDLAGLRDAIALQGGDPAQVNPVVPTQLIVDH 120
Query: 121 SLAVECGGFDPDAFAKNRAIEDRRNEDRFHFIDWTKQAFKNVDVIPPGNGIMHQINLEKM 180
SLAVE GG DP AFAKNRAIEDRRNEDRFHFI+WTK+AFKNVDVIPPGNGIMHQINLEKM
Sbjct: 121 SLAVESGGADPQAFAKNRAIEDRRNEDRFHFINWTKKAFKNVDVIPPGNGIMHQINLEKM 180
Query: 181 SPVIHADNGVAYPDTCVGTDSHTPHVDALGVIAIGVGGLEAENVMLGRASWMRLPDIVGV 240
SPVI +GVA+PDTCVGTDSHTPHVDALGVIAIGVGGLEAE+VMLGRASWMRLP+IVGV
Sbjct: 181 SPVIQQRDGVAFPDTCVGTDSHTPHVDALGVIAIGVGGLEAESVMLGRASWMRLPEIVGV 240
Query: 241 ELTGKRQPGITATDIVLALTEFLRKEKVVGAYLEFRGEGASSLTLGDRATISNMAPEYGA 300
ELTGK QPGITATD+VLALTEFLRK+KVVGA+LEF GEGAS+LTLGDR TISNMAPEYGA
Sbjct: 241 ELTGKLQPGITATDMVLALTEFLRKQKVVGAWLEFFGEGASALTLGDRVTISNMAPEYGA 300
Query: 301 TAAMFFIDEQTIDYLRLTGRTDEQLKLVETYARTAGLWADSLKNAEYERVLKFDLSSVVR 360
TAAMF ID+QTIDYL+LTGR D Q++LVETYA+ GLWADSLK A+YER L FDLSSVVR
Sbjct: 301 TAAMFHIDQQTIDYLKLTGREDTQVQLVETYAKHVGLWADSLKGAQYERGLTFDLSSVVR 360
Query: 361 NMAGPSNPHKRLPTSALAERGIAVDLDKASAQEAEGLMPDGAVIIAAITSCTNTSNPRNV 420
NMAGPSNPH R+ S LA +GI+ D + G MPDGAVIIAAITSCTNTSNPRNV
Sbjct: 361 NMAGPSNPHARVAVSELAAKGISGQWD-----DVPGQMPDGAVIIAAITSCTNTSNPRNV 415
Query: 421 IAAALLARNANARGLARKPWVKSSLAPGSKAVELYLEEANLLPDLEKLGFGIVAFACTTC 480
IAA LLARNAN GLARKPWVKSSLAPGSK V LYL+EA L +LEKLGFG+VAFACTTC
Sbjct: 416 IAAGLLARNANRLGLARKPWVKSSLAPGSKTVALYLDEAGLTSELEKLGFGVVAFACTTC 475
Query: 481 NGMSGALDPKIQQEIIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTI 540
NGMSGALDP IQQEIIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTI
Sbjct: 476 NGMSGALDPVIQQEIIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTI 535
Query: 541 RFDIEKDVLGTDQDGKPVYLKDIWPSDEEIDAIVAKSVKPEQFRKVYEPMFAITAASGES 600
RFDIEKDVLG DG+ + LKDIWPSDEEIDA+V SVKPEQFR+VY PMFAI +G
Sbjct: 536 RFDIEKDVLGV-VDGREIRLKDIWPSDEEIDAVVKASVKPEQFRQVYIPMFAIQEDTGPK 594
Query: 601 VSPLYDWRPQSTYIRRPPYWEGALAGERTLKALRPLAVLGDNITTDHLSPSNAIMLNSAA 660
V+PLYDWRPQSTYIRRPPYWEGALAG R LK +RPLAVL DNITTDHLSPSNAIML+SAA
Sbjct: 595 VTPLYDWRPQSTYIRRPPYWEGALAGARPLKGMRPLAVLPDNITTDHLSPSNAIMLDSAA 654
Query: 661 GEYLARMGLPEEDFNSYATHRGDHLTAQRATFANPTLINEMAVVDGQVKKGSLARIEPEG 720
GEYLA+MGLPEEDFNSYATHRGDHLTAQRATFANP L NEM +G+VK+GSLAR+EPEG
Sbjct: 655 GEYLAKMGLPEEDFNSYATHRGDHLTAQRATFANPKLFNEMVQENGKVKQGSLARVEPEG 714
Query: 721 KVVRMWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEVIVAEGFERIHRTN 780
KV+RMWEAIETYM+RKQPLIIIAGADYGQGSSRDWAAKGVRLAGVE I AEGFERIHRTN
Sbjct: 715 KVMRMWEAIETYMERKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEAIAAEGFERIHRTN 774
Query: 781 LIGMGVLPLEFKPGVNRLTLGLDGTETYDVIGERQPRATLTLVVNRKNGERVEVPVTCRL 840
L+GMGVLPLEFKPG +R TLG+DG+E YDVIGER PRATLTLV+ RKNGERVEVPVTCRL
Sbjct: 775 LVGMGVLPLEFKPGTDRKTLGIDGSEVYDVIGERTPRATLTLVITRKNGERVEVPVTCRL 834
Query: 841 DSDEEVSIYEAGGVL-HFAQDFLESSRA 867
D+ EEVSIYEAGGVL FAQDFLES+ A
Sbjct: 835 DTAEEVSIYEAGGVLQRFAQDFLESAVA 862
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: 2210
Number of extensions: 84
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: 863
Length adjustment: 42
Effective length of query: 827
Effective length of database: 821
Effective search space: 678967
Effective search space used: 678967
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 AO356_20875 AO356_20875 (Fe/S-dependent 2-methylisocitrate dehydratase AcnD)
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.20629.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 1826.9 0.0 0 1826.7 0.0 1.0 1 lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_20875 AO356_20875 Fe/S-dependent 2-met
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_20875 AO356_20875 Fe/S-dependent 2-methylisocitrate dehydratase AcnD
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1826.7 0.0 0 0 1 858 [] 2 858 .. 2 858 .. 1.00
Alignments for each domain:
== domain 1 score: 1826.7 bits; conditional E-value: 0
TIGR02333 1 ntkyrkalpgtdldyfdaraaveaikpgaydklpytsrvlaenlvrrvdpetleaslkqlier 63
nt++rk+lpgt+ldyfd r av+ai+pgayd lpytsrvlaenlvrr+dp+tl +sl qlier
lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_20875 2 NTEFRKPLPGTSLDYFDVRGAVDAIRPGAYDGLPYTSRVLAENLVRRCDPATLRESLLQLIER 64
899************************************************************ PP
TIGR02333 64 kreldfpwyparvvchdilgqtalvdlaglrdaiaekggdpaqvnpvvetqlivdhslaveyg 126
kr+ldfpw+parvvchdilgqtalvdlaglrdaia +ggdpaqvnpvv+tqlivdhslave g
lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_20875 65 KRDLDFPWFPARVVCHDILGQTALVDLAGLRDAIALQGGDPAQVNPVVPTQLIVDHSLAVESG 127
*************************************************************** PP
TIGR02333 127 gfdpdafeknraiedrrnedrfhfinwtkkafknvdvipagngimhqinlekmspvvqvkegv 189
g dp+af+knraiedrrnedrfhfinwtkkafknvdvip+gngimhqinlekmspv+q ++gv
lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_20875 128 GADPQAFAKNRAIEDRRNEDRFHFINWTKKAFKNVDVIPPGNGIMHQINLEKMSPVIQQRDGV 190
*************************************************************** PP
TIGR02333 190 afpdtlvgtdshtphvdalgviaigvggleaetvmlgraslmrlpdivgveltgkrqpgitat 252
afpdt+vgtdshtphvdalgviaigvggleae+vmlgras+mrlp+ivgveltgk qpgitat
lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_20875 191 AFPDTCVGTDSHTPHVDALGVIAIGVGGLEAESVMLGRASWMRLPEIVGVELTGKLQPGITAT 253
*************************************************************** PP
TIGR02333 253 divlalteflrkekvvsayleffgegakaltlgdratisnmtpeygataamfaideqtidylk 315
d+vlalteflrk+kvv+a+leffgega altlgdr tisnm+peygataamf id+qtidylk
lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_20875 254 DMVLALTEFLRKQKVVGAWLEFFGEGASALTLGDRVTISNMAPEYGATAAMFHIDQQTIDYLK 316
*************************************************************** PP
TIGR02333 316 ltgreeeqvklvetyakaaglwadslkkavyervlkfdlssvvrnlagpsnpharlatsdlaa 378
ltgre+ qv+lvetyak glwadslk a+yer l+fdlssvvrn+agpsnphar+a s+laa
lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_20875 317 LTGREDTQVQLVETYAKHVGLWADSLKGAQYERGLTFDLSSVVRNMAGPSNPHARVAVSELAA 379
*************************************************************** PP
TIGR02333 379 kgiakeveeeaeglmpdgaviiaaitsctntsnprnvvaagllarnanklglkrkpwvkssla 441
kgi++++++++ g+mpdgaviiaaitsctntsnprnv+aagllarnan+lgl rkpwvkssla
lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_20875 380 KGISGQWDDVP-GQMPDGAVIIAAITSCTNTSNPRNVIAAGLLARNANRLGLARKPWVKSSLA 441
***********.*************************************************** PP
TIGR02333 442 pgskvvklyleeagllkeleklgfgivafacttcngmsgaldpviqqeiidrdlyatavlsgn 504
pgsk+v lyl+eagl +eleklgfg+vafacttcngmsgaldpviqqeiidrdlyatavlsgn
lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_20875 442 PGSKTVALYLDEAGLTSELEKLGFGVVAFACTTCNGMSGALDPVIQQEIIDRDLYATAVLSGN 504
*************************************************************** PP
TIGR02333 505 rnfdgrihpyakqaflaspplvvayaiagtirfdiekdvlgvdadgkeirlkdiwpsdeeida 567
rnfdgrihpyakqaflaspplvvayaiagtirfdiekdvlgv +dg+eirlkdiwpsdeeida
lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_20875 505 RNFDGRIHPYAKQAFLASPPLVVAYAIAGTIRFDIEKDVLGV-VDGREIRLKDIWPSDEEIDA 566
******************************************.******************** PP
TIGR02333 568 vvaaavkpeqfrkvyipmfdle.daqkkvsplydwrpmstyirrppywegalagertlkgmrp 629
vv+a+vkpeqfr+vyipmf+++ d++ kv+plydwrp+styirrppywegalag r lkgmrp
lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_20875 567 VVKASVKPEQFRQVYIPMFAIQeDTGPKVTPLYDWRPQSTYIRRPPYWEGALAGARPLKGMRP 629
*********************989*************************************** PP
TIGR02333 630 lavlgdnittdhlspsnailldsaageylakmglpeedfnsyathrgdhltaqratfanpklf 692
lavl+dnittdhlspsnai+ldsaageylakmglpeedfnsyathrgdhltaqratfanpklf
lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_20875 630 LAVLPDNITTDHLSPSNAIMLDSAAGEYLAKMGLPEEDFNSYATHRGDHLTAQRATFANPKLF 692
*************************************************************** PP
TIGR02333 693 nemvkedgkvkqgslariepegkvtrmweaietymnrkqpliiiagadygqgssrdwaakgvr 755
nemv+e+gkvkqgslar+epegkv+rmweaietym+rkqpliiiagadygqgssrdwaakgvr
lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_20875 693 NEMVQENGKVKQGSLARVEPEGKVMRMWEAIETYMERKQPLIIIAGADYGQGSSRDWAAKGVR 755
*************************************************************** PP
TIGR02333 756 lagveaivaegferihrtnlvgmgvlplefkpgtnrktlaldgtevydvvgeitpradltlvv 818
lagveai aegferihrtnlvgmgvlplefkpgt+rktl++dg+evydv+ge+tpra+ltlv+
lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_20875 756 LAGVEAIAAEGFERIHRTNLVGMGVLPLEFKPGTDRKTLGIDGSEVYDVIGERTPRATLTLVI 818
*************************************************************** PP
TIGR02333 819 trkngeklevpvtcrldtaeevsvyeaggvlqrfaqdfle 858
trknge++evpvtcrldtaeevs+yeaggvlqrfaqdfle
lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_20875 819 TRKNGERVEVPVTCRLDTAEEVSIYEAGGVLQRFAQDFLE 858
**************************************97 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (858 nodes)
Target sequences: 1 (863 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: 0.04u 0.02s 00:00:00.06 Elapsed: 00:00:00.06
# Mc/sec: 11.78
//
[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