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 AZOBR_RS02985 AZOBR_RS02985 aconitate hydratase
Query= SwissProt::P37032
(891 letters)
>FitnessBrowser__azobra:AZOBR_RS02985
Length = 896
Score = 1201 bits (3107), Expect = 0.0
Identities = 593/890 (66%), Positives = 706/890 (79%), Gaps = 3/890 (0%)
Query: 4 GQDSLSTKSQLTVDGKTYNYYSLKEAENKHFKGINRLPYSLKVLLENLLRFEDGNTVTTK 63
GQDSL T+ L+V GK+Y+Y+S+K AE+ ++RLPYS+KVLLENLLRFEDG TV+T
Sbjct: 6 GQDSLKTRRSLSVGGKSYDYFSIKAAEDAGLGDLSRLPYSMKVLLENLLRFEDGRTVSTD 65
Query: 64 DIKAIADWLHNKTSQHEIAFRPTRVLMQDFTGVPAVVDLAAMRTAIVKMGGNADKISPLS 123
D+KA+A WLH+K S EIA+RP RVLMQDFTGVPAV DLAAMR A+ +GG+ KI+PL
Sbjct: 66 DVKAVAQWLHDKRSDREIAYRPARVLMQDFTGVPAVCDLAAMREAMAALGGDPKKINPLV 125
Query: 124 PVDLVIDHSVMVDKFASADALEVNTKIEIERNKERYEFLRWGQKAFSNFQVVPPGTGICH 183
PVDLVIDHSVMVD F + A E N ++E ERN ERY FLRWGQKAF NF+VVPPGTGICH
Sbjct: 126 PVDLVIDHSVMVDYFGNPSAFEKNVELEFERNLERYAFLRWGQKAFDNFRVVPPGTGICH 185
Query: 184 QVNLEYLGKTVW-NSENDGQLYAYPDTLVGTDSHTTMINGLGVLGWGVGGIEAEAAMLGQ 242
QVN+EYL + VW +++ G+L AYPDTLVGTDSHTTM+NGLGVLGWGVGGIEAEAAMLGQ
Sbjct: 186 QVNVEYLAQGVWTDTDPAGKLVAYPDTLVGTDSHTTMVNGLGVLGWGVGGIEAEAAMLGQ 245
Query: 243 PVSMLIPEVIGFKLSGKLKEGITATDLVLTVTQMLRKKGVVGKFVEFYGPGLNDLPLADR 302
P+SMLIPEV+GFKL+G+LKEG TATDLVLTVTQMLRKKGVVGKFVEFYGPGL+ L LADR
Sbjct: 246 PISMLIPEVVGFKLTGRLKEGTTATDLVLTVTQMLRKKGVVGKFVEFYGPGLDHLTLADR 305
Query: 303 ATISNMAPEYGATCGFFPVDKETIKYLELTGRDKHTIALVEAYAKAQGMWYDKDNEEPVF 362
ATI NMAPEYGATCG FP+D ETI+YL TGRD +A+VEAYA+AQGMW D +PVF
Sbjct: 306 ATIGNMAPEYGATCGIFPIDAETIRYLTFTGRDADRVAMVEAYARAQGMWRDAGTPDPVF 365
Query: 363 TDSLHLDLGSVEPSLAGPKRPQDKVNLSSLPVEFNNFLIEVGKEKEKEKTFAVKNKDFQM 422
TD+L LD+ +VEPSLAGPKRPQD+V LS F L+ K ++ +++ VK + +
Sbjct: 366 TDALELDMTTVEPSLAGPKRPQDRVPLSQAAQSFGTDLVGAFKAEDADRSVPVKGCGYNL 425
Query: 423 KHGHVVIAAITSCTNTSNPSVLMAAGLVAKKAIEKGLQRKPWVKSSLAPGSKVVTDYLRH 482
G VVIAAITSCTNTSNP+VL+AAGL+A+KA+EKGL+ KPWVK+SLAPGS+VVTDYL
Sbjct: 426 DQGAVVIAAITSCTNTSNPAVLVAAGLLARKAVEKGLKSKPWVKTSLAPGSQVVTDYLAK 485
Query: 483 AGLQTYLDQLGFNLVGYGCTTCIGNSGPLPDDISHCVAEHDLVVSSVLSGNRNFEGRVHP 542
AGLQ YLDQLGFN+VGYGCTTCIGNSGPLPD I+ V E +LVV++VLSGNRNFEGRV+P
Sbjct: 486 AGLQPYLDQLGFNIVGYGCTTCIGNSGPLPDPIAAAVEEGNLVVAAVLSGNRNFEGRVNP 545
Query: 543 QVRANWLASPPLVVAYALCGTTCSDLSREPIGQDKEGNDVYLKDIWPSNEEIAAEV-AKV 601
RAN+LASPPL VAYAL G DL+++PIG +G VYLKD+WP+N+E+ + A +
Sbjct: 546 HTRANYLASPPLCVAYALAGNMKIDLAKDPIGTGHDGQPVYLKDVWPTNQEVQDAIDASL 605
Query: 602 SGTMFRKEYAEVFKGDAHWQAIQTSSGQTYEWNPDSTYIQHPPFFENLSLKPEPLKPIKQ 661
S MFR Y VF+G W+ IQT+ GQTYEW STY++ PPFF ++ P+ + ++
Sbjct: 606 SAEMFRSRYGNVFEGPEQWRGIQTAEGQTYEWQAGSTYVKLPPFFADMPKTPDAVSDVRG 665
Query: 662 AYVLALFGDSITTDHISPAGSIKASSPAGLYLKSKGVDEKDFNSYGSRRGNHEVMMRGTF 721
A LA+ GDSITTDHISPAGSIK +SPAG YL S V +DFNSYG+RRGNHEVMMRGTF
Sbjct: 666 ARALAVLGDSITTDHISPAGSIKKTSPAGEYLLSHQVRPQDFNSYGARRGNHEVMMRGTF 725
Query: 722 ANIRIRNEMTPGQEGGVTRYVPTGETMSIYDAAMRYQENQQDLVIIAGKEYGTGSSRDWA 781
ANIRIRNEM G EGG TR+ P+GE + IY AAMRY + LV+IAGKEYGTGSSRDWA
Sbjct: 726 ANIRIRNEMLAGVEGGETRHYPSGEQLPIYTAAMRYAQEGVPLVVIAGKEYGTGSSRDWA 785
Query: 782 AKGTNLLGVKAVITESFERIHRSNLIGMGILPLQFKEGTTRKTLKLDGSERISIE-ISDK 840
AKGT LLG++AVI ESFERIHRSNL+GMGILPLQFK+G TR L LDG+E I+ I
Sbjct: 786 AKGTKLLGIRAVIAESFERIHRSNLVGMGILPLQFKDGLTRNDLALDGTETFDIDGIEQD 845
Query: 841 LTPGAMVPVTIERQDGDIEKIETLCRIDTADELEYYKNGGILQYVLRKIS 890
L P V +TI R DG ++ L RIDT DE+EYY+NGG+L +VLR ++
Sbjct: 846 LRPRKDVTMTITRADGQTRQVPLLLRIDTVDEVEYYRNGGVLNFVLRNLA 895
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: 2142
Number of extensions: 82
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: 891
Length of database: 896
Length adjustment: 43
Effective length of query: 848
Effective length of database: 853
Effective search space: 723344
Effective search space used: 723344
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 AZOBR_RS02985 AZOBR_RS02985 (aconitate hydratase)
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.24771.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 1409.9 0.0 0 1409.7 0.0 1.0 1 lcl|FitnessBrowser__azobra:AZOBR_RS02985 AZOBR_RS02985 aconitate hydratas
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__azobra:AZOBR_RS02985 AZOBR_RS02985 aconitate hydratase
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1409.7 0.0 0 0 2 875 .. 22 894 .. 21 895 .. 0.98
Alignments for each domain:
== domain 1 score: 1409.7 bits; conditional E-value: 0
TIGR01341 2 kvyyyslkalees.lekisklpkslrillesvlrnldgskikeedveallkwkkeelkdeeiafkparv 69
++ y+s+ka+e++ l+++s+lp+s+++lle++lr dg++++ +dv+a+++w +++ +d+eia++parv
lcl|FitnessBrowser__azobra:AZOBR_RS02985 22 SYDYFSIKAAEDAgLGDLSRLPYSMKVLLENLLRFEDGRTVSTDDVKAVAQWLHDKRSDREIAYRPARV 90
789********99789***************************************************** PP
TIGR01341 70 vlqdftGvpavvdlaalreavknlgkdpekinplvpvdlvidhsvqvdkageeealeanvelefernke 138
++qdftGvpav dlaa+rea+++lg+dp+kinplvpvdlvidhsv vd++g+ +a+e+nvelefern e
lcl|FitnessBrowser__azobra:AZOBR_RS02985 91 LMQDFTGVPAVCDLAAMREAMAALGGDPKKINPLVPVDLVIDHSVMVDYFGNPSAFEKNVELEFERNLE 159
********************************************************************* PP
TIGR01341 139 rykflkwakkafknlkvvppgtGivhqvnleylakvvfe.aekdgellaypdslvGtdshttminGlGv 206
ry+fl+w++kaf n++vvppgtGi+hqvn+eyla+ v++ ++ g+l+aypd+lvGtdshttm+nGlGv
lcl|FitnessBrowser__azobra:AZOBR_RS02985 160 RYAFLRWGQKAFDNFRVVPPGTGICHQVNVEYLAQGVWTdTDPAGKLVAYPDTLVGTDSHTTMVNGLGV 228
***********************************999725568************************* PP
TIGR01341 207 lGwGvGGieaeaallGqpvslsvpeviGvkltGklreGvtatdlvltvtellrkkgvvgkfveffGegl 275
lGwGvGGieaeaa+lGqp+s+ +pev+G+kltG+l+eG+tatdlvltvt++lrkkgvvgkfvef+G+gl
lcl|FitnessBrowser__azobra:AZOBR_RS02985 229 LGWGVGGIEAEAAMLGQPISMLIPEVVGFKLTGRLKEGTTATDLVLTVTQMLRKKGVVGKFVEFYGPGL 297
********************************************************************* PP
TIGR01341 276 kelsladratianmapeyGataaffpiddvtlqylrltgrdedkvelvekylkaqelfvd.dseepkyt 343
++l+ladrati nmapeyGat+++fpid++t+ yl tgrd d+v +ve+y++aq++++d + +p++t
lcl|FitnessBrowser__azobra:AZOBR_RS02985 298 DHLTLADRATIGNMAPEYGATCGIFPIDAETIRYLTFTGRDADRVAMVEAYARAQGMWRDaGTPDPVFT 366
************************************************************66678**** PP
TIGR01341 344 dvveldlsdveasvaGpkrpqdrvalkevkaafksslesnagekglalrkeakekklegkeaelkdgav 412
d +eld+ +ve+s+aGpkrpqdrv+l++ ++f + l ++ ++ ++g ++l++gav
lcl|FitnessBrowser__azobra:AZOBR_RS02985 367 DALELDMTTVEPSLAGPKRPQDRVPLSQAAQSFGTDLVGAFKAED-----ADRSVPVKGCGYNLDQGAV 430
**********************************99986554444.....5566677899********* PP
TIGR01341 413 viaaitsctntsnpsvllgagllakkavelGlkvkpyvktslapGskvvtdylaesgllpyleelGfnl 481
viaaitsctntsnp+vl++aglla+kave Glk kp+vktslapGs+vvtdyla++gl+pyl++lGfn+
lcl|FitnessBrowser__azobra:AZOBR_RS02985 431 VIAAITSCTNTSNPAVLVAAGLLARKAVEKGLKSKPWVKTSLAPGSQVVTDYLAKAGLQPYLDQLGFNI 499
********************************************************************* PP
TIGR01341 482 vGyGcttciGnsGpleeeveeaikendlevsavlsGnrnfegrihplvkanylaspplvvayalaGtvd 550
vGyGcttciGnsGpl++ ++ a+ e++l+v+avlsGnrnfegr++p ++anylasppl vayalaG+++
lcl|FitnessBrowser__azobra:AZOBR_RS02985 500 VGYGCTTCIGNSGPLPDPIAAAVEEGNLVVAAVLSGNRNFEGRVNPHTRANYLASPPLCVAYALAGNMK 568
********************************************************************* PP
TIGR01341 551 idlekepigtdkdGkkvylkdiwpsakeiaelvkkavkkelfkkeyeevtegnerwnelevtssdlyew 619
idl+k+pigt++dG++vylkd+wp+++e++++++ +++ e+f+ +y +v+eg e+w+ ++++++++yew
lcl|FitnessBrowser__azobra:AZOBR_RS02985 569 IDLAKDPIGTGHDGQPVYLKDVWPTNQEVQDAIDASLSAEMFRSRYGNVFEGPEQWRGIQTAEGQTYEW 637
********************************************************************* PP
TIGR01341 620 dekstyireppffeelklepeevedikgarillllGdsittdhispaGsikkdspaakylkekGverrd 688
+ sty+++ppff ++ +p+ v+d++gar l++lGdsittdhispaGsikk spa++yl + v ++d
lcl|FitnessBrowser__azobra:AZOBR_RS02985 638 QAGSTYVKLPPFFADMPKTPDAVSDVRGARALAVLGDSITTDHISPAGSIKKTSPAGEYLLSHQVRPQD 706
********************************************************************* PP
TIGR01341 689 fnsyGsrrGnhevmlrGtfaniriknklvkgkeGgltvylpdsevvsvydaamkykkegvplvvlaGke 757
fnsyG+rrGnhevm+rGtfaniri+n+++ g eGg t+++p +e++ +y aam+y +egvplvv+aGke
lcl|FitnessBrowser__azobra:AZOBR_RS02985 707 FNSYGARRGNHEVMMRGTFANIRIRNEMLAGVEGGETRHYPSGEQLPIYTAAMRYAQEGVPLVVIAGKE 775
********************************************************************* PP
TIGR01341 758 yGsGssrdwaakgtkllGvkaviaesferihrsnlvgmGvlplefkqgedaetlgltgeetidvddi.e 825
yG+GssrdwaakgtkllG++aviaesferihrsnlvgmG+lpl+fk+g +++ l l+g+et d+d+i +
lcl|FitnessBrowser__azobra:AZOBR_RS02985 776 YGTGSSRDWAAKGTKLLGIRAVIAESFERIHRSNLVGMGILPLQFKDGLTRNDLALDGTETFDIDGIeQ 844
******************************************************************835 PP
TIGR01341 826 elkpkkevtvelvkedgeketveavlridtevelayvkkgGilqyvlrkl 875
+l+p+k+vt++++++dg+ + v lridt e++y+++gG+l++vlr+l
lcl|FitnessBrowser__azobra:AZOBR_RS02985 845 DLRPRKDVTMTITRADGQTRQVPLLLRIDTVDEVEYYRNGGVLNFVLRNL 894
8***********************************************96 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (876 nodes)
Target sequences: 1 (896 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: 0.05u 0.03s 00:00:00.08 Elapsed: 00:00:00.38
# Mc/sec: 2.05
//
[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