Align aconitate hydratase (EC 4.2.1.3) (characterized)
to candidate WP_011765266.1 AZO_RS07750 aconitate hydratase AcnA
Query= BRENDA::A0A090AMG4
(901 letters)
>NCBI__GCF_000061505.1:WP_011765266.1
Length = 903
Score = 1184 bits (3063), Expect = 0.0
Identities = 594/896 (66%), Positives = 715/896 (79%), Gaps = 10/896 (1%)
Query: 8 TLKNFKI-GNKSCQYYSLPALGKSLGID-VQRLPVSIRIVLESVLRNCDGKKVTEEHVKQ 65
TLK F G + +Y+SLPAL ++ GI V RLPVS+RIVLE+VLR CDG KV EHV+Q
Sbjct: 13 TLKTFTTPGGEIGRYFSLPAL-EAAGIGPVSRLPVSLRIVLEAVLRRCDGLKVDIEHVRQ 71
Query: 66 LANWQANARREDEIPFVVARVVLQDFTGVPLLADIAAMRSVADKMGKSPKSIEPLVPVDL 125
LANW+ R EIPFVVARVVLQDFTGVPLL D+AAMR VA + G+ PK IEPLVPVDL
Sbjct: 72 LANWEPGGERCAEIPFVVARVVLQDFTGVPLLCDLAAMRDVAAEQGRDPKRIEPLVPVDL 131
Query: 126 VVDHSVMIDYFGTKNALDLNMKLEFKRNQERYQFMKWGMQAFDTFGVVPPGFGIVHQVNL 185
VVDHSV +D++G+ AL NM+LEF+RN+ERYQF+KWGMQAFDTFGVVPPG GIVHQ+NL
Sbjct: 132 VVDHSVQVDHYGSPIALRQNMELEFERNRERYQFLKWGMQAFDTFGVVPPGIGIVHQINL 191
Query: 186 EYLARGVHLDKKNNVYYPDSLVGTDSHTTMINGIGVVGWGVGGIEAEAGMLGQPVYFLTP 245
EYL RG L ++ ++YYPD+LVGTDSHTTMING+GVVGWGVGGIEAEA MLGQPVYFLTP
Sbjct: 192 EYLFRG--LREEGDLYYPDTLVGTDSHTTMINGLGVVGWGVGGIEAEAAMLGQPVYFLTP 249
Query: 246 DVVGVELKGQLRGGVTATDLVLTITEMLRREKVVGKFVEFCGEGTASLSVAERATIGNMA 305
DV+GVEL+G+L GVTATDLVLT+TE+LRREKVVGKFVEF G+GTA+L+V +RATI NMA
Sbjct: 250 DVIGVELRGKLPEGVTATDLVLTVTELLRREKVVGKFVEFFGDGTANLTVTDRATIANMA 309
Query: 306 PEYGATMGFFPVDERTIDYFRGTGRTEAEIAAFEAYFKAQKMFGVPKAADINFTKLLTLD 365
PEYGATMGFFPVDE+++ Y RGTGR E A EA+F+AQ+MFGVP+A +I++T+ L LD
Sbjct: 310 PEYGATMGFFPVDEKSVAYMRGTGRDERNCALLEAWFRAQQMFGVPRAGEIDYTRTLVLD 369
Query: 366 LSTVAPSLAGPKRPQDRIEIGNVKNTFIDLYSKPVAENGFNQPAEKLAQTFTTS-AGTQV 424
L+T+ PS+AGPKRPQDRI +G + F +L+S P A NGF +PAE L + + +
Sbjct: 370 LATITPSVAGPKRPQDRIPLGGLGARFTELFSAPTAANGFGRPAETLRERVPSGRENIAL 429
Query: 425 KNGDILIAAITSCTNTSNPSVLLAAGLLAKKAVEAGLTVPKHIKTSLAPGSRVVTEYLTK 484
NGD+LIAAITSCTNTSNP+VL+AAGLLA+KAVEAGL V HIKTSLAPGSRVVT+YL K
Sbjct: 430 GNGDVLIAAITSCTNTSNPAVLIAAGLLARKAVEAGLRVQPHIKTSLAPGSRVVTDYLEK 489
Query: 485 TGLLPYLEKLGFDVAAYGCTTCIGNAGDLTPDLNEAIIGNDLICSAVLSGNRNFEARIHP 544
GLL L +LGF +A YGCTTCIGNAGDL P+ NE I + L+ +AVLSGNRNFEARIHP
Sbjct: 490 AGLLEPLAELGFALAGYGCTTCIGNAGDLAPEFNETIAAHHLVAAAVLSGNRNFEARIHP 549
Query: 545 NIKANFLASPPLVVAYALAGTVTRDLMTEPVGRGKNG-DVWLGDIWPTTEEIESLLKYAL 603
+I+ANFLASPPLVVA+ALAGTV DL +P+G G NG V+L D+WP+++EI +++ A+
Sbjct: 550 SIRANFLASPPLVVAFALAGTVNIDLTRDPLGTGHNGKPVFLRDLWPSSDEIAAVMPLAM 609
Query: 604 DPKAFEANYGQVKSNPGKLWENTKGVTGDTYNWPDSTYIAEPPFFEGFGMTPGAMPAVKG 663
DP + Y + + LW G Y+WP STYIA PPFF GFGMTP A++
Sbjct: 610 DPANYRQRYADL-TRDHDLWNAIAAPAGQRYDWPPSTYIARPPFFTGFGMTPQPTTAIRS 668
Query: 664 ARALGVFGDSVTTDHISPAGSIKETSPAGKWLKENGVMKADFNSYGSRRGNHEIMMRGTF 723
A AL + GDSVTTDHISPAGS +ET+PAG+WL GV + DFNSYGSRRG+HE+MMRGTF
Sbjct: 669 AHALLLLGDSVTTDHISPAGSFRETTPAGQWLSAQGVARKDFNSYGSRRGHHEVMMRGTF 728
Query: 724 ANVRIKNLMIPALPDGSRFEGGETLFQPTGEQMSIYDAAMKYVSAGTPTVVFGGEEYGTG 783
ANVRI+NLM+PA DG+R EGG TL G+ ++Y+AAM Y GTPT++F GEEYGTG
Sbjct: 729 ANVRIRNLMLPADGDGNRMEGGYTLLD--GQLTTVYEAAMAYQQRGTPTLIFAGEEYGTG 786
Query: 784 SSRDWAAKGTQLLGVKAVITRSFERIHRSNLVGMGVLPLQFKGADSVQSLGITGEETYDI 843
SSRDWAAKGT LLGV+AVI RSFERIHRSNLVGMGVLPLQFKG DS +LG+ G E +D+
Sbjct: 787 SSRDWAAKGTALLGVRAVIARSFERIHRSNLVGMGVLPLQFKGEDSWPALGLDGSEQFDL 846
Query: 844 SGLEDGIKPMQDVTLTITRKDGSKQDVTVLLRIDTPIEVDYYQHGGILPFVLRQLL 899
GL+ ++P+QDVTL I R DG + V + RIDTPIEV+YY+HGGILP+VLR++L
Sbjct: 847 DGLDGELRPLQDVTLVIHRADGDTRRVVLQCRIDTPIEVEYYRHGGILPYVLREIL 902
Lambda K H
0.317 0.136 0.400
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: 2303
Number of extensions: 94
Number of successful extensions: 6
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: 901
Length of database: 903
Length adjustment: 43
Effective length of query: 858
Effective length of database: 860
Effective search space: 737880
Effective search space used: 737880
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 WP_011765266.1 AZO_RS07750 (aconitate hydratase AcnA)
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.18818.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 1240.9 0.0 0 1240.7 0.0 1.0 1 lcl|NCBI__GCF_000061505.1:WP_011765266.1 AZO_RS07750 aconitate hydratase
Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000061505.1:WP_011765266.1 AZO_RS07750 aconitate hydratase AcnA
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1240.7 0.0 0 0 4 876 .] 26 902 .. 23 902 .. 0.97
Alignments for each domain:
== domain 1 score: 1240.7 bits; conditional E-value: 0
TIGR01341 4 yyyslkalees.lekisklpkslrillesvlrnldgskikeedveallkwkkeelkdeeiafkparvvl 71
y+sl+ale + ++ +s+lp slri+le+vlr++dg k+ e+v +l++w+ + ei+f +arvvl
lcl|NCBI__GCF_000061505.1:WP_011765266.1 26 RYFSLPALEAAgIGPVSRLPVSLRIVLEAVLRRCDGLKVDIEHVRQLANWEPGGERCAEIPFVVARVVL 94
7*******9887899****************************************************** PP
TIGR01341 72 qdftGvpavvdlaalreavknlgkdpekinplvpvdlvidhsvqvdkageeealeanvelefernkery 140
qdftGvp++ dlaa+r+ ++ g+dp++i+plvpvdlv+dhsvqvd++g+ al++n+elefern+ery
lcl|NCBI__GCF_000061505.1:WP_011765266.1 95 QDFTGVPLLCDLAAMRDVAAEQGRDPKRIEPLVPVDLVVDHSVQVDHYGSPIALRQNMELEFERNRERY 163
********************************************************************* PP
TIGR01341 141 kflkwakkafknlkvvppgtGivhqvnleylakvvfeaekdgellaypdslvGtdshttminGlGvlGw 209
+flkw+ +af + vvppg Givhq+nleyl + + e+ +l ypd+lvGtdshttminGlGv+Gw
lcl|NCBI__GCF_000061505.1:WP_011765266.1 164 QFLKWGMQAFDTFGVVPPGIGIVHQINLEYLFRGLREEG----DLYYPDTLVGTDSHTTMINGLGVVGW 228
*******************************88765544....788*********************** PP
TIGR01341 210 GvGGieaeaallGqpvslsvpeviGvkltGklreGvtatdlvltvtellrkkgvvgkfveffGeglkel 278
GvGGieaeaa+lGqpv++ p+viGv l Gkl eGvtatdlvltvtellr++ vvgkfveffG+g ++l
lcl|NCBI__GCF_000061505.1:WP_011765266.1 229 GVGGIEAEAAMLGQPVYFLTPDVIGVELRGKLPEGVTATDLVLTVTELLRREKVVGKFVEFFGDGTANL 297
********************************************************************* PP
TIGR01341 279 sladratianmapeyGataaffpiddvtlqylrltgrdedkvelvekylkaqelfvd.dseepkytdvv 346
+++dratianmapeyGat++ffp+d++++ y+r tgrde + l+e++ +aq++f + e+ yt+++
lcl|NCBI__GCF_000061505.1:WP_011765266.1 298 TVTDRATIANMAPEYGATMGFFPVDEKSVAYMRGTGRDERNCALLEAWFRAQQMFGVpRAGEIDYTRTL 366
*******************************************************988999******** PP
TIGR01341 347 eldlsdveasvaGpkrpqdrvalkevkaafksslesnagekglalrkeakekkle..gkeaelkdgavv 413
ldl ++ +svaGpkrpqdr++l + a f++ ++ +++ +g++ + e+ ++ + ++ l +g+v
lcl|NCBI__GCF_000061505.1:WP_011765266.1 367 VLDLATITPSVAGPKRPQDRIPLGGLGARFTELFSAPTAANGFGRPAETLRERVPsgRENIALGNGDVL 435
*********************************************99988888765467899******* PP
TIGR01341 414 iaaitsctntsnpsvllgagllakkavelGlkvkpyvktslapGskvvtdylaesgllpyleelGfnlv 482
iaaitsctntsnp+vl++aglla+kave+Gl+v+p++ktslapGs+vvtdyl ++gll+ l elGf l
lcl|NCBI__GCF_000061505.1:WP_011765266.1 436 IAAITSCTNTSNPAVLIAAGLLARKAVEAGLRVQPHIKTSLAPGSRVVTDYLEKAGLLEPLAELGFALA 504
********************************************************************* PP
TIGR01341 483 GyGcttciGnsGpleeeveeaikendlevsavlsGnrnfegrihplvkanylaspplvvayalaGtvdi 551
GyGcttciGn+G+l e +e+i+ +l+++avlsGnrnfe+rihp ++an+laspplvva+alaGtv+i
lcl|NCBI__GCF_000061505.1:WP_011765266.1 505 GYGCTTCIGNAGDLAPEFNETIAAHHLVAAAVLSGNRNFEARIHPSIRANFLASPPLVVAFALAGTVNI 573
********************************************************************* PP
TIGR01341 552 dlekepigtdkdGkkvylkdiwpsakeiaelvkkavkkelfkkeyeevtegnerwnelevtssdlyewd 620
dl+++p+gt+++Gk+v+l+d+wps +eia+++ a+ + ++++y+ +t + + wn + ++ ++ y+w
lcl|NCBI__GCF_000061505.1:WP_011765266.1 574 DLTRDPLGTGHNGKPVFLRDLWPSSDEIAAVMPLAMDPANYRQRYADLTRDHDLWNAIAAPAGQRYDWP 642
********************************************************************6 PP
TIGR01341 621 ekstyireppffeelklepeevedikgarillllGdsittdhispaGsikkdspaakylkekGverrdf 689
styi +ppff ++ ++p+ + i+ a+ llllGds+ttdhispaGs ++ +pa+++l +Gv r+df
lcl|NCBI__GCF_000061505.1:WP_011765266.1 643 -PSTYIARPPFFTGFGMTPQPTTAIRSAHALLLLGDSVTTDHISPAGSFRETTPAGQWLSAQGVARKDF 710
.59****************************************************************** PP
TIGR01341 690 nsyGsrrGnhevmlrGtfaniriknklvkg......keGgltvylpdsevvsvydaamkykkegvplvv 752
nsyGsrrG hevm+rGtfan+ri+n ++++ eGg+t+ d++ ++vy+aam y++ g+p+++
lcl|NCBI__GCF_000061505.1:WP_011765266.1 711 NSYGSRRGHHEVMMRGTFANVRIRNLMLPAdgdgnrMEGGYTL--LDGQLTTVYEAAMAYQQRGTPTLI 777
***************************9852222334788875..69********************** PP
TIGR01341 753 laGkeyGsGssrdwaakgtkllGvkaviaesferihrsnlvgmGvlplefkqgedaetlgltgeetidv 821
aG+eyG+Gssrdwaakgt llGv+avia+sferihrsnlvgmGvlpl+fk ++ +lgl+g+e+ d+
lcl|NCBI__GCF_000061505.1:WP_011765266.1 778 FAGEEYGTGSSRDWAAKGTALLGVRAVIARSFERIHRSNLVGMGVLPLQFKGEDSWPALGLDGSEQFDL 846
********************************************************************* PP
TIGR01341 822 ddie.elkpkkevtvelvkedgeketveavlridtevelayvkkgGilqyvlrkll 876
d+++ el+p ++vt+++ ++dg+ + v ++ridt++e++y+++gGil yvlr++l
lcl|NCBI__GCF_000061505.1:WP_011765266.1 847 DGLDgELRPLQDVTLVIHRADGDTRRVVLQCRIDTPIEVEYYRHGGILPYVLREIL 902
**8549***********************************************986 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (876 nodes)
Target sequences: 1 (903 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 0.02s 00:00:00.07 Elapsed: 00:00:00.06
# Mc/sec: 12.12
//
[ok]
This GapMind analysis is from Sep 24 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