Align Aconitate hydratase A; ACN; Aconitase; (2R,3S)-2-methylisocitrate dehydratase; (2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate dehydratase; IP210; Iron-responsive protein-like; IRP-like; Major iron-containing protein; MICP; Probable 2-methyl-cis-aconitate hydratase; RNA-binding protein; EC 4.2.1.3; EC 4.2.1.99 (characterized)
to candidate Ga0059261_3296 Ga0059261_3296 aconitate hydratase 1
Query= SwissProt::P37032
(891 letters)
>FitnessBrowser__Korea:Ga0059261_3296
Length = 890
Score = 1149 bits (2972), Expect = 0.0
Identities = 585/891 (65%), Positives = 688/891 (77%), Gaps = 8/891 (0%)
Query: 3 VGQDSLSTKSQLTVDGKTYNYYSLKEAENKHFKGINRLPYSLKVLLENLLRFEDGNTVTT 62
+GQDSL T+ LTV GK+Y+YYSL++A K ++RLP+S+KVLLEN+LRFEDG TVT
Sbjct: 4 IGQDSLGTRETLTVGGKSYSYYSLEKAAAK-LGDVSRLPFSMKVLLENMLRFEDGVTVTP 62
Query: 63 KDIKAIADWLHNKTS-QHEIAFRPTRVLMQDFTGVPAVVDLAAMRTAIVKMGGNADKISP 121
+D +AI DW N + + EI +RP RVLMQDFTGVP VVDLAAMR AI K+GG+A KI+P
Sbjct: 63 EDAQAIVDWQKNPNAPEREIQYRPARVLMQDFTGVPCVVDLAAMRDAITKLGGDAAKINP 122
Query: 122 LSPVDLVIDHSVMVDKFASADALEVNTKIEIERNKERYEFLRWGQKAFSNFQVVPPGTGI 181
PV LVIDHSVMVD+F + A E N ++E +RN ERY+FL+WG K+ NF+VVPPGTGI
Sbjct: 123 QVPVHLVIDHSVMVDEFGTPKAFEENVELEYQRNMERYDFLKWGSKSLDNFKVVPPGTGI 182
Query: 182 CHQVNLEYLGKTVWNSEN-DGQLYAYPDTLVGTDSHTTMINGLGVLGWGVGGIEAEAAML 240
CHQVNLEY+ +W+S DG AYPDTLVGTDSHTTM+NGLGVLGWGVGGIEAEAAML
Sbjct: 183 CHQVNLEYIADAIWSSTAADGTTVAYPDTLVGTDSHTTMVNGLGVLGWGVGGIEAEAAML 242
Query: 241 GQPVSMLIPEVIGFKLSGKLKEGITATDLVLTVTQMLRKKGVVGKFVEFYGPGLNDLPLA 300
GQPVSMLIPEV+GFKL+GKL+EGITATDLVLTVTQMLR +GVVG+FVEF+GPGL + LA
Sbjct: 243 GQPVSMLIPEVVGFKLTGKLQEGITATDLVLTVTQMLRARGVVGRFVEFFGPGLATMTLA 302
Query: 301 DRATISNMAPEYGATCGFFPVDKETIKYLELTGRDKHTIALVEAYAKAQGMWYDKDNEEP 360
DRATI+NMAPEYGATCGFF +D +T+ Y+ LTGRD T+ LVEAY KAQGMW D +P
Sbjct: 303 DRATIANMAPEYGATCGFFGIDDKTLDYMRLTGRDDDTVTLVEAYCKAQGMWRYDDMADP 362
Query: 361 VFTDSLHLDLGSVEPSLAGPKRPQDKVNLSSLPVEFNNFLIEVGKEKEKEKTFAVKNKDF 420
+FTD+L LD+ +V SLAGPKRPQD+V+L+ + FN L +V KE AV+ KD
Sbjct: 363 IFTDTLELDMATVTASLAGPKRPQDRVSLNKVDEVFNGDLFKV-YGKENGHRVAVEGKDH 421
Query: 421 QMKHGHVVIAAITSCTNTSNPSVLMAAGLVAKKAIEKGLQRKPWVKSSLAPGSKVVTDYL 480
+ G VVIAAITSCTNTSNPSVL+AAGLVA+KA KGL RKPWVK+SLAPGS+VVTDYL
Sbjct: 422 DIGDGDVVIAAITSCTNTSNPSVLIAAGLVARKARAKGLTRKPWVKTSLAPGSQVVTDYL 481
Query: 481 RHAGLQTYLDQLGFNLVGYGCTTCIGNSGPLPDDISHCVAEHDLVVSSVLSGNRNFEGRV 540
AGL LD +GFNLVGYGCTTCIGNSGPL IS + +D+V +SVLSGNRNFEGRV
Sbjct: 482 NKAGLSEDLDAIGFNLVGYGCTTCIGNSGPLAQPISDAINGNDIVAASVLSGNRNFEGRV 541
Query: 541 HPQVRANWLASPPLVVAYALCGTTCSDLSREPIGQDKEGNDVYLKDIWPSNEEIAAEV-A 599
P VRAN+LASPPLVVAYAL GT D+ PIG+ +G VYLKDIWP+NEE+ + A
Sbjct: 542 SPDVRANFLASPPLVVAYALKGTVTEDMIETPIGEGTDG-PVYLKDIWPTNEEVQGVINA 600
Query: 600 KVSGTMFRKEYAEVFKGDAHWQAIQTSSGQTYEWNPDSTYIQHPPFFENLSLKPEPLKPI 659
+ MF+ Y V+ GDAHWQ I TY W STYI +PP+F +++ P P+ I
Sbjct: 601 NIDSEMFKSRYGNVYLGDAHWQKINVEGSATYSWPAASTYIANPPYFAGMTMTPAPVADI 660
Query: 660 KQAYVLALFGDSITTDHISPAGSIKASSPAGLYLKSKGVDEKDFNSYGSRRGNHEVMMRG 719
A LA+ GDSITTDHISPAGSIKA SPAG +L + V + DFNSYG+RRGN VM+RG
Sbjct: 661 VDAKPLAILGDSITTDHISPAGSIKADSPAGKWLMERQVSKADFNSYGARRGNDNVMVRG 720
Query: 720 TFANIRIRNEMTPGQEGGVTRYVPTGETMSIYDAAMRYQENQQDLVIIAGKEYGTGSSRD 779
TFANIRIRNEM PG EGG+T Y GETM IYDAAMR++ + LVI+AGKEYGTGSSRD
Sbjct: 721 TFANIRIRNEMVPGVEGGMTSY--AGETMPIYDAAMRHKADGTPLVIVAGKEYGTGSSRD 778
Query: 780 WAAKGTNLLGVKAVITESFERIHRSNLIGMGILPLQFKEGTTRKTLKLDGSERISIEISD 839
WAAKGTNLLGV+AVITESFERIHRSNL+GMG+LPLQF EG TR+TLKLDGSE +I
Sbjct: 779 WAAKGTNLLGVRAVITESFERIHRSNLVGMGVLPLQFAEGVTRQTLKLDGSETFTITGVA 838
Query: 840 KLTPGAMVPVTIERQDGDIEKIETLCRIDTADELEYYKNGGILQYVLRKIS 890
L P V V + R DG E T CRIDT +ELEY+ NGGILQYVLR ++
Sbjct: 839 GLRPRQDVEVKLTRADGSSETFLTRCRIDTVNELEYFLNGGILQYVLRNLA 889
Lambda K H
0.316 0.134 0.393
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: 2101
Number of extensions: 88
Number of successful extensions: 8
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: 891
Length of database: 890
Length adjustment: 43
Effective length of query: 848
Effective length of database: 847
Effective search space: 718256
Effective search space used: 718256
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 (21.6 bits)
S2: 56 (26.2 bits)
Align candidate Ga0059261_3296 Ga0059261_3296 (aconitate hydratase 1)
to HMM TIGR01341 (acnA: aconitate hydratase 1 (EC 4.2.1.3))
# 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/TIGR01341.hmm
# target sequence database: /tmp/gapView.1788519.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: TIGR01341 [M=876]
Accession: TIGR01341
Description: aconitase_1: aconitate hydratase 1
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 1361.1 0.0 0 1360.9 0.0 1.0 1 lcl|FitnessBrowser__Korea:Ga0059261_3296 Ga0059261_3296 aconitate hydrata
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Korea:Ga0059261_3296 Ga0059261_3296 aconitate hydratase 1
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1360.9 0.0 0 0 1 875 [. 20 888 .. 20 889 .. 0.98
Alignments for each domain:
== domain 1 score: 1360.9 bits; conditional E-value: 0
TIGR01341 1 kkvyyyslkaleeslekisklpkslrillesvlrnldgskikeedveallkwkke.elkdeeiafkpar 68
k++ yysl++++ +l+++s+lp s+++lle++lr dg +++ ed +a+++w+k+ + ++ei+++par
lcl|FitnessBrowser__Korea:Ga0059261_3296 20 KSYSYYSLEKAAAKLGDVSRLPFSMKVLLENMLRFEDGVTVTPEDAQAIVDWQKNpNAPEREIQYRPAR 88
5789************************************************998345689******** PP
TIGR01341 69 vvlqdftGvpavvdlaalreavknlgkdpekinplvpvdlvidhsvqvdkageeealeanvelefernk 137
v++qdftGvp vvdlaa+r+a+++lg+d++kinp+vpv lvidhsv vd++g+ +a+e+nvele++rn+
lcl|FitnessBrowser__Korea:Ga0059261_3296 89 VLMQDFTGVPCVVDLAAMRDAITKLGGDAAKINPQVPVHLVIDHSVMVDEFGTPKAFEENVELEYQRNM 157
********************************************************************* PP
TIGR01341 138 erykflkwakkafknlkvvppgtGivhqvnleylakvvfe.aekdgellaypdslvGtdshttminGlG 205
ery flkw++k++ n+kvvppgtGi+hqvnley+a+++++ + dg ++aypd+lvGtdshttm+nGlG
lcl|FitnessBrowser__Korea:Ga0059261_3296 158 ERYDFLKWGSKSLDNFKVVPPGTGICHQVNLEYIADAIWSsTAADGTTVAYPDTLVGTDSHTTMVNGLG 226
**************************************972568************************* PP
TIGR01341 206 vlGwGvGGieaeaallGqpvslsvpeviGvkltGklreGvtatdlvltvtellrkkgvvgkfveffGeg 274
vlGwGvGGieaeaa+lGqpvs+ +pev+G+kltGkl+eG+tatdlvltvt++lr +gvvg+fveffG+g
lcl|FitnessBrowser__Korea:Ga0059261_3296 227 VLGWGVGGIEAEAAMLGQPVSMLIPEVVGFKLTGKLQEGITATDLVLTVTQMLRARGVVGRFVEFFGPG 295
********************************************************************* PP
TIGR01341 275 lkelsladratianmapeyGataaffpiddvtlqylrltgrdedkvelvekylkaqelfvd.dseepky 342
l++++ladratianmapeyGat++ff idd+tl+y+rltgrd+d+v lve+y+kaq++++ d ++p++
lcl|FitnessBrowser__Korea:Ga0059261_3296 296 LATMTLADRATIANMAPEYGATCGFFGIDDKTLDYMRLTGRDDDTVTLVEAYCKAQGMWRYdDMADPIF 364
***********************************************************754999**** PP
TIGR01341 343 tdvveldlsdveasvaGpkrpqdrvalkevkaafksslesnagekglalrkeakekklegkeaelkdga 411
td++eld+ +v as+aGpkrpqdrv+l++v++ f+ l + g+++ ++ ++egk++ + dg+
lcl|FitnessBrowser__Korea:Ga0059261_3296 365 TDTLELDMATVTASLAGPKRPQDRVSLNKVDEVFNGDLFKVYGKEN------GHRVAVEGKDHDIGDGD 427
***********************************99988777665......6677889********** PP
TIGR01341 412 vviaaitsctntsnpsvllgagllakkavelGlkvkpyvktslapGskvvtdylaesgllpyleelGfn 480
vviaaitsctntsnpsvl++agl+a+ka Gl +kp+vktslapGs+vvtdyl+++gl + l+++Gfn
lcl|FitnessBrowser__Korea:Ga0059261_3296 428 VVIAAITSCTNTSNPSVLIAAGLVARKARAKGLTRKPWVKTSLAPGSQVVTDYLNKAGLSEDLDAIGFN 496
********************************************************************* PP
TIGR01341 481 lvGyGcttciGnsGpleeeveeaikendlevsavlsGnrnfegrihplvkanylaspplvvayalaGtv 549
lvGyGcttciGnsGpl + +++ai+ nd+++++vlsGnrnfegr+ p+v+an+laspplvvayal Gtv
lcl|FitnessBrowser__Korea:Ga0059261_3296 497 LVGYGCTTCIGNSGPLAQPISDAINGNDIVAASVLSGNRNFEGRVSPDVRANFLASPPLVVAYALKGTV 565
********************************************************************* PP
TIGR01341 550 didlekepigtdkdGkkvylkdiwpsakeiaelvkkavkkelfkkeyeevtegnerwnelevtssdlye 618
+ d+ + pig ++dG +vylkdiwp+++e++ +++ ++ +e+fk +y +v g+++w++++v s++y+
lcl|FitnessBrowser__Korea:Ga0059261_3296 566 TEDMIETPIGEGTDG-PVYLKDIWPTNEEVQGVINANIDSEMFKSRYGNVYLGDAHWQKINVEGSATYS 633
**************9.8**************************************************** PP
TIGR01341 619 wdekstyireppffeelklepeevedikgarillllGdsittdhispaGsikkdspaakylkekGverr 687
w styi +pp+f +++++p+ v di +a+ l+ lGdsittdhispaGsik dspa+k+l+e+ v++
lcl|FitnessBrowser__Korea:Ga0059261_3296 634 WPAASTYIANPPYFAGMTMTPAPVADIVDAKPLAILGDSITTDHISPAGSIKADSPAGKWLMERQVSKA 702
********************************************************************* PP
TIGR01341 688 dfnsyGsrrGnhevmlrGtfaniriknklvkgkeGgltvylpdsevvsvydaamkykkegvplvvlaGk 756
dfnsyG+rrGn++vm+rGtfaniri+n++v+g eGg+t y +e++ +ydaam++k +g+plv++aGk
lcl|FitnessBrowser__Korea:Ga0059261_3296 703 DFNSYGARRGNDNVMVRGTFANIRIRNEMVPGVEGGMTSYA--GETMPIYDAAMRHKADGTPLVIVAGK 769
****************************************6..689*********************** PP
TIGR01341 757 eyGsGssrdwaakgtkllGvkaviaesferihrsnlvgmGvlplefkqgedaetlgltgeetidvddie 825
eyG+Gssrdwaakgt+llGv+avi+esferihrsnlvgmGvlpl+f +g +++tl l+g+et + ++
lcl|FitnessBrowser__Korea:Ga0059261_3296 770 EYGTGSSRDWAAKGTNLLGVRAVITESFERIHRSNLVGMGVLPLQFAEGVTRQTLKLDGSETFTITGVA 838
********************************************************************* PP
TIGR01341 826 elkpkkevtvelvkedgeketveavlridtevelayvkkgGilqyvlrkl 875
l+p+++v+v+l+++dg+ et+ +++ridt el+y+ +gGilqyvlr+l
lcl|FitnessBrowser__Korea:Ga0059261_3296 839 GLRPRQDVEVKLTRADGSSETFLTRCRIDTVNELEYFLNGGILQYVLRNL 888
************************************************96 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (876 nodes)
Target sequences: 1 (890 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 39.68
//
[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