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.2779.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: 0.06u 0.03s 00:00:00.09 Elapsed: 00:00:00.08
# Mc/sec: 8.35
//
[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