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.18317.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: 0.08u 0.02s 00:00:00.10 Elapsed: 00:00:00.09
# Mc/sec: 8.21
//
[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