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 6939202 Sama_3296 aconitate hydratase (RefSeq)
Query= SwissProt::Q937N8
(869 letters)
>FitnessBrowser__SB2B:6939202
Length = 861
Score = 1407 bits (3641), Expect = 0.0
Identities = 703/867 (81%), Positives = 768/867 (88%), Gaps = 8/867 (0%)
Query: 1 MNSANRKPLPGTKLDYFDARAAVEAIQPGAYDKLPYTSRVLAENLVRRCDPATLTDSLLQ 60
MN+ RKPLPGT L +FD R AV+AI PGA+DKLPYTS+VLAENL+R+ +PA L D L Q
Sbjct: 1 MNTQFRKPLPGTNLSFFDTREAVDAIAPGAFDKLPYTSKVLAENLLRKAEPARLNDFLSQ 60
Query: 61 LVGRKRDLDFPWFPARVVCHDILGQTALVDLAGLRDAIADQGGDPAKVNPVVPVQLIVDH 120
L+ RK+DLDFPWFPARVVCHDILGQTALVDLAGLRDAIA +GGDPAKVNPVVP QLIVDH
Sbjct: 61 LIFRKQDLDFPWFPARVVCHDILGQTALVDLAGLRDAIAAKGGDPAKVNPVVPTQLIVDH 120
Query: 121 SLAVECGGFDPDAFAKNRAIEDRRNEDRFHFIDWTKQAFKNVDVIPPGNGIMHQINLEKM 180
SLAVE GGF+ DAF KNRAIEDRRN+DRFHFI+WTK+AF+NVDVIPPGNGIMHQINLEKM
Sbjct: 121 SLAVEHGGFEKDAFEKNRAIEDRRNDDRFHFINWTKKAFRNVDVIPPGNGIMHQINLEKM 180
Query: 181 SPVIHADNGVAYPDTCVGTDSHTPHVDALGVIAIGVGGLEAENVMLGRASWMRLPDIVGV 240
SPVI +G+A+PDTCVGTDSHTPHVD+LGVIAIGVGGLEAENVMLGRASWMRLPDIVGV
Sbjct: 181 SPVIQVRDGIAFPDTCVGTDSHTPHVDSLGVIAIGVGGLEAENVMLGRASWMRLPDIVGV 240
Query: 241 ELTGKRQPGITATDIVLALTEFLRKEKVVGAYLEFRGEGASSLTLGDRATISNMAPEYGA 300
ELTGK PGITATD+VLALTEFLRKE+VVGAYLEF GEGA +LTLGDRATISNM PEYGA
Sbjct: 241 ELTGKPNPGITATDVVLALTEFLRKERVVGAYLEFFGEGAKALTLGDRATISNMTPEYGA 300
Query: 301 TAAMFFIDEQTIDYLRLTGRTDEQLKLVETYARTAGLWADSLKNAEYERVLKFDLSSVVR 360
TAAMF+IDEQTIDYLRLTGR ++Q++LVE YA+T GLWAD++ A+Y R+L FDLSSVVR
Sbjct: 301 TAAMFYIDEQTIDYLRLTGRDEKQVELVENYAKTTGLWADAMTGADYGRILTFDLSSVVR 360
Query: 361 NMAGPSNPHKRLPTSALAERGIAVDLDKASAQEAEGLMPDGAVIIAAITSCTNTSNPRNV 420
NMAGPSNPH RL TS LA +GIA D QE G MPDGAVIIAAITSCTNTSNPRNV
Sbjct: 361 NMAGPSNPHARLATSDLAAKGIAADW-----QEESGKMPDGAVIIAAITSCTNTSNPRNV 415
Query: 421 IAAALLARNANARGLARKPWVKSSLAPGSKAVELYLEEANLLPDLEKLGFGIVAFACTTC 480
IAA L+ARNA +GL RKPWVK+SLAPGSKAVELYL+EA LLP LE+LGFGIVAFACTTC
Sbjct: 416 IAAGLIARNAVQKGLVRKPWVKTSLAPGSKAVELYLKEAGLLPYLEQLGFGIVAFACTTC 475
Query: 481 NGMSGALDPKIQQEIIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTI 540
NGMSGALDP IQQEII+RDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGT+
Sbjct: 476 NGMSGALDPVIQQEIIERDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTV 535
Query: 541 RFDIEKDVLGTDQDGKPVYLKDIWPSDEEIDAIVAKSVKPEQFRKVYEPMFAITAASGES 600
RFDIEKDVLG D G V LKD+WP D EIDAI+ SVKPEQFR VY+PMF + G +
Sbjct: 536 RFDIEKDVLGIDDAGNAVTLKDLWPEDAEIDAIIKSSVKPEQFRAVYDPMFNLAVEYG-T 594
Query: 601 VSPLYDWRPQSTYIRRPPYWEGALAGERTLKALRPLAVLGDNITTDHLSPSNAIMLNSAA 660
PLYDWRPQSTYIRRPPYWEGALAGERTL +RPLAVLGDNITTDHLSPSNAI+ +SAA
Sbjct: 595 EKPLYDWRPQSTYIRRPPYWEGALAGERTLSGMRPLAVLGDNITTDHLSPSNAILASSAA 654
Query: 661 GEYLARMGLPEEDFNSYATHRGDHLTAQRATFANPTLINEMAV-VDGQVKKGSLARIEPE 719
GEYLA+MGLPEEDFNSYATHRGDHLTAQRATFANP L NEM DG+VK+GSLAR+EPE
Sbjct: 655 GEYLAKMGLPEEDFNSYATHRGDHLTAQRATFANPKLFNEMVKDADGKVKQGSLARLEPE 714
Query: 720 GKVVRMWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEVIVAEGFERIHRT 779
GKV+RMWE IETYM+RKQPLII+AG DYGQGSSRDWAAKGVRLAGVEVIVAEGFERIHRT
Sbjct: 715 GKVLRMWETIETYMERKQPLIIVAGKDYGQGSSRDWAAKGVRLAGVEVIVAEGFERIHRT 774
Query: 780 NLIGMGVLPLEFKPGVNRLTLGLDGTETYDVIGERQPRATLTLVVNRKNGERVEVPVTCR 839
NL+GMGVLPLEF PG R+T G+DGTET+DV GER P A LTL++ R+NGE VEVPV CR
Sbjct: 775 NLVGMGVLPLEFMPGETRMTYGIDGTETFDVKGERTPGAELTLLIRRQNGETVEVPVRCR 834
Query: 840 LDSDEEVSIYEAGGVL-HFAQDFLESS 865
LD+ EEVSIYEAGGVL FAQDFL +S
Sbjct: 835 LDTAEEVSIYEAGGVLQRFAQDFLANS 861
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: 2229
Number of extensions: 96
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: 861
Length adjustment: 42
Effective length of query: 827
Effective length of database: 819
Effective search space: 677313
Effective search space used: 677313
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 6939202 Sama_3296 (aconitate hydratase (RefSeq))
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.21799.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 1770.0 0.0 0 1769.8 0.0 1.0 1 lcl|FitnessBrowser__SB2B:6939202 Sama_3296 aconitate hydratase (R
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__SB2B:6939202 Sama_3296 aconitate hydratase (RefSeq)
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1769.8 0.0 0 0 1 858 [] 2 859 .. 2 859 .. 1.00
Alignments for each domain:
== domain 1 score: 1769.8 bits; conditional E-value: 0
TIGR02333 1 ntkyrkalpgtdldyfdaraaveaikpgaydklpytsrvlaenlvrrvdpetleaslkqlierkreldfpwyparvv 77
nt++rk+lpgt+l +fd+r+av+ai+pga+dklpyts+vlaenl+r+++p++l+++l+qli rk++ldfpw+parvv
lcl|FitnessBrowser__SB2B:6939202 2 NTQFRKPLPGTNLSFFDTREAVDAIAPGAFDKLPYTSKVLAENLLRKAEPARLNDFLSQLIFRKQDLDFPWFPARVV 78
89*************************************************************************** PP
TIGR02333 78 chdilgqtalvdlaglrdaiaekggdpaqvnpvvetqlivdhslaveyggfdpdafeknraiedrrnedrfhfinwt 154
chdilgqtalvdlaglrdaia+kggdpa+vnpvv+tqlivdhslave ggf++dafeknraiedrrn+drfhfinwt
lcl|FitnessBrowser__SB2B:6939202 79 CHDILGQTALVDLAGLRDAIAAKGGDPAKVNPVVPTQLIVDHSLAVEHGGFEKDAFEKNRAIEDRRNDDRFHFINWT 155
***************************************************************************** PP
TIGR02333 155 kkafknvdvipagngimhqinlekmspvvqvkegvafpdtlvgtdshtphvdalgviaigvggleaetvmlgraslm 231
kkaf+nvdvip+gngimhqinlekmspv+qv++g+afpdt+vgtdshtphvd+lgviaigvggleae+vmlgras+m
lcl|FitnessBrowser__SB2B:6939202 156 KKAFRNVDVIPPGNGIMHQINLEKMSPVIQVRDGIAFPDTCVGTDSHTPHVDSLGVIAIGVGGLEAENVMLGRASWM 232
***************************************************************************** PP
TIGR02333 232 rlpdivgveltgkrqpgitatdivlalteflrkekvvsayleffgegakaltlgdratisnmtpeygataamfaide 308
rlpdivgveltgk +pgitatd+vlalteflrke+vv+ayleffgegakaltlgdratisnmtpeygataamf+ide
lcl|FitnessBrowser__SB2B:6939202 233 RLPDIVGVELTGKPNPGITATDVVLALTEFLRKERVVGAYLEFFGEGAKALTLGDRATISNMTPEYGATAAMFYIDE 309
***************************************************************************** PP
TIGR02333 309 qtidylkltgreeeqvklvetyakaaglwadslkkavyervlkfdlssvvrnlagpsnpharlatsdlaakgiakev 385
qtidyl+ltgr+e+qv+lve yak++glwad++ a y r+l+fdlssvvrn+agpsnpharlatsdlaakgia ++
lcl|FitnessBrowser__SB2B:6939202 310 QTIDYLRLTGRDEKQVELVENYAKTTGLWADAMTGADYGRILTFDLSSVVRNMAGPSNPHARLATSDLAAKGIAADW 386
***************************************************************************** PP
TIGR02333 386 eeeaeglmpdgaviiaaitsctntsnprnvvaagllarnanklglkrkpwvksslapgskvvklyleeagllkelek 462
+ee+ g+mpdgaviiaaitsctntsnprnv+aagl+arna ++gl rkpwvk+slapgsk+v+lyl+eagll+ le+
lcl|FitnessBrowser__SB2B:6939202 387 QEES-GKMPDGAVIIAAITSCTNTSNPRNVIAAGLIARNAVQKGLVRKPWVKTSLAPGSKAVELYLKEAGLLPYLEQ 462
***9.************************************************************************ PP
TIGR02333 463 lgfgivafacttcngmsgaldpviqqeiidrdlyatavlsgnrnfdgrihpyakqaflaspplvvayaiagtirfdi 539
lgfgivafacttcngmsgaldpviqqeii+rdlyatavlsgnrnfdgrihpyakqaflaspplvvayaiagt+rfdi
lcl|FitnessBrowser__SB2B:6939202 463 LGFGIVAFACTTCNGMSGALDPVIQQEIIERDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTVRFDI 539
***************************************************************************** PP
TIGR02333 540 ekdvlgvdadgkeirlkdiwpsdeeidavvaaavkpeqfrkvyipmfdledaqkkvsplydwrpmstyirrppyweg 616
ekdvlg+d g+ + lkd+wp d+eida+++++vkpeqfr vy pmf+l + + plydwrp+styirrppyweg
lcl|FitnessBrowser__SB2B:6939202 540 EKDVLGIDDAGNAVTLKDLWPEDAEIDAIIKSSVKPEQFRAVYDPMFNLAVEYGTEKPLYDWRPQSTYIRRPPYWEG 616
**************************************************8888899******************** PP
TIGR02333 617 alagertlkgmrplavlgdnittdhlspsnailldsaageylakmglpeedfnsyathrgdhltaqratfanpklfn 693
alagertl gmrplavlgdnittdhlspsnail++saageylakmglpeedfnsyathrgdhltaqratfanpklfn
lcl|FitnessBrowser__SB2B:6939202 617 ALAGERTLSGMRPLAVLGDNITTDHLSPSNAILASSAAGEYLAKMGLPEEDFNSYATHRGDHLTAQRATFANPKLFN 693
***************************************************************************** PP
TIGR02333 694 emvked.gkvkqgslariepegkvtrmweaietymnrkqpliiiagadygqgssrdwaakgvrlagveaivaegfer 769
emvk+ gkvkqgslar+epegkv rmwe+ietym+rkqplii+ag dygqgssrdwaakgvrlagve ivaegfer
lcl|FitnessBrowser__SB2B:6939202 694 EMVKDAdGKVKQGSLARLEPEGKVLRMWETIETYMERKQPLIIVAGKDYGQGSSRDWAAKGVRLAGVEVIVAEGFER 770
****866********************************************************************** PP
TIGR02333 770 ihrtnlvgmgvlplefkpgtnrktlaldgtevydvvgeitpradltlvvtrkngeklevpvtcrldtaeevsvyeag 846
ihrtnlvgmgvlplef pg+ r t+++dgte++dv ge+tp+a+ltl+++r+nge++evpv crldtaeevs+yeag
lcl|FitnessBrowser__SB2B:6939202 771 IHRTNLVGMGVLPLEFMPGETRMTYGIDGTETFDVKGERTPGAELTLLIRRQNGETVEVPVRCRLDTAEEVSIYEAG 847
***************************************************************************** PP
TIGR02333 847 gvlqrfaqdfle 858
gvlqrfaqdfl+
lcl|FitnessBrowser__SB2B:6939202 848 GVLQRFAQDFLA 859
**********95 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (858 nodes)
Target sequences: 1 (861 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: 12.04
//
[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