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.23243.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: 0.07u 0.02s 00:00:00.09 Elapsed: 00:00:00.09
# Mc/sec: 8.18
//
[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