Align Aconitate hydratase (EC 4.2.1.3) (characterized)
to candidate WP_043529276.1 JH15_RS08095 aconitate hydratase AcnA
Query= reanno::Marino:GFF3491
(919 letters)
>NCBI__GCF_000759345.1:WP_043529276.1
Length = 914
Score = 1419 bits (3674), Expect = 0.0
Identities = 691/917 (75%), Positives = 802/917 (87%), Gaps = 6/917 (0%)
Query: 6 LSKDSL-NTLSSLDAGGKTFHYYSLPKAADTLGDLNRLPFSLKVLMENLLRNEDGTTVDR 64
+S DS NTL+SL G + +HYYSLPKAA+ LGD+ RLP +LK+L+EN LR D +V R
Sbjct: 1 MSADSAPNTLASLTVGEREYHYYSLPKAAEALGDIQRLPVTLKILLENQLRFADDESVSR 60
Query: 65 SHIDAMVQWMKDRHSDTEIQFRPARVLMQDFTGVPGVVDLAAMREAVQAAGKDPAMINPL 124
+ A+V W ++ S EI +RPARVLMQDFTGVPGVVDLA+MR AV+ G+DP+ INPL
Sbjct: 61 EDMQALVDWQQEARSTREIGYRPARVLMQDFTGVPGVVDLASMRAAVEKLGEDPSRINPL 120
Query: 125 SPVDLVIDHSVMVDKFGDASSFKDNVAIEMERNQERYEFLRWGQQAFDNFRVVPPGTGIC 184
SPVDLVIDHSVMVDK+GD S+F+DNVAIEM+RN+ERYEFLRWGQ AFDNFRVVPPGTGIC
Sbjct: 121 SPVDLVIDHSVMVDKYGDPSAFRDNVAIEMDRNRERYEFLRWGQDAFDNFRVVPPGTGIC 180
Query: 185 HQVNLEYLGKTVWQKDQDGKTIAYPDTLVGTDSHTTMINGLGILGWGVGGIEAEAAMLGQ 244
HQVNLEYLGKTVW K++DGK+ AYPDTLVGTDSHTTMINGLG+LGWGVGGIEAEAAMLGQ
Sbjct: 181 HQVNLEYLGKTVWVKEEDGKSFAYPDTLVGTDSHTTMINGLGVLGWGVGGIEAEAAMLGQ 240
Query: 245 PVSMLIPEVVGFKITGKLREGITATDLVLTVTEMLRKKGVVGKFVEFYGDGLKDMPVADR 304
PVSMLIPEVVGFK+TGKLREGITATDLVLTVT+MLR+KGVVGKFVEFYGDGL D+P+ADR
Sbjct: 241 PVSMLIPEVVGFKLTGKLREGITATDLVLTVTQMLRQKGVVGKFVEFYGDGLDDLPLADR 300
Query: 305 ATIANMAPEYGATCGFFPVDEQTIKYMRLTGREEEQLELVEAYAKAQGLWREPGHEPVYT 364
ATIANMAPEYGATCGFFPVD++T+ Y+RLTGR +E++ LVEAY K Q LWR+PG EPV++
Sbjct: 301 ATIANMAPEYGATCGFFPVDDETLNYLRLTGRSDEEVALVEAYCKEQDLWRKPGAEPVFS 360
Query: 365 DNLELDMGEVEASLAGPKRPQDRVALKNMKSSFELLM--ETAEGPAENREANLESEGGQT 422
D L+LDMG+VEASLAGPKRPQDRVAL +MKS+FE LM + AE A R +SEGGQ
Sbjct: 361 DTLQLDMGDVEASLAGPKRPQDRVALSDMKSTFENLMGDDAAEASATAR-GKFDSEGGQM 419
Query: 423 AVGVDDSYKHHASQPLEMNGEKSRLDPGAVVIAAITSCTNTSNPSVMMAAGLIAQKAVQK 482
VG + ++HH SQ +++ G +L+PGAVVIAAITSCTNTSNPSVMMAAGL+A+KAV+K
Sbjct: 420 PVGTHEHFEHHDSQDVDVEGSTFKLNPGAVVIAAITSCTNTSNPSVMMAAGLLARKAVEK 479
Query: 483 GLSTKPWVKTSLAPGSKVVTDYLKVGGFQDDLDKLGFNLVGYGCTTCIGNSGPLPDAVEK 542
GL TKPWVKTSLAPGSKVVTDYL GGFQDDL+ LGFNLVGYGCTTCIGNSGPL +EK
Sbjct: 480 GLDTKPWVKTSLAPGSKVVTDYLAAGGFQDDLNALGFNLVGYGCTTCIGNSGPLLPPIEK 539
Query: 543 AISDGDLTVASVLSGNRNFEGRVHPLVKTNWLASPPLVVAYALAGNVRLDLSQDPLGNDK 602
AI DGDLTVASVLSGNRNFEGRVHPLVKTNWLASPPLVVAYALAGNVRLD+S++PLG K
Sbjct: 540 AIEDGDLTVASVLSGNRNFEGRVHPLVKTNWLASPPLVVAYALAGNVRLDISKEPLGEGK 599
Query: 603 DGNPVYLKDLWPSQQEIAEAVEKVKTDMFRKEYAEVFDGDATWKSIKVPESKVYEWSDKS 662
DG PVYL+D+WPSQ EIAEAVEKV+T+M+RKEYAEVF+GD WK+I VP+S+VY+WS+ S
Sbjct: 600 DGKPVYLQDIWPSQAEIAEAVEKVRTEMYRKEYAEVFEGDEVWKAIDVPQSQVYQWSEDS 659
Query: 663 TYIQHPPFFEGLKEEPDAIDDIKDANILALLGDSVTTDHISPAGSFKPDTPAGKYLQEHG 722
TYIQHPPFFEG+ EP+ + D+++A +LA+LGDSVTTDHISPAG+ KPD+PAG+YLQEHG
Sbjct: 660 TYIQHPPFFEGMGREPEPLQDVENARVLAMLGDSVTTDHISPAGAIKPDSPAGRYLQEHG 719
Query: 723 VEPKDFNSYGSRRGNHEVMMRGTFANVRIRNEMLDGVEGGYTKFVPTGEQMAIYDAAMKY 782
V+P DFNSYGSRRGNHEVMMRGTFANVRIRNEMLDGVEGGYT+ VP+ EQMAIYDAAMKY
Sbjct: 720 VKPMDFNSYGSRRGNHEVMMRGTFANVRIRNEMLDGVEGGYTRHVPSDEQMAIYDAAMKY 779
Query: 783 QEKGTPLVVIAGKEYGTGSSRDWAAKGTRLLGVKAVVAESYERIHRSNLIGMGVMPLQFP 842
E+G PLVVIAGKEYGTGSSRDWAAKGTRLLGV+AV+AESYERIHRSNLIGMGV+PLQFP
Sbjct: 780 AEEGRPLVVIAGKEYGTGSSRDWAAKGTRLLGVRAVLAESYERIHRSNLIGMGVVPLQFP 839
Query: 843 EGTDRKSLKLTGEETISIEGLSGEIKPGQTLKMTVKYKDGSTETCELKSRIDTANEAVYF 902
EG DRKSL LTG+E +SI+G++ ++ PG + +T+K D + E RIDTANE Y+
Sbjct: 840 EGEDRKSLGLTGDEEVSIDGIA-DLTPGGQVNVTIK-SDKGEKKIEALCRIDTANELEYY 897
Query: 903 KHGGILHYVVREMLRTA 919
+HGGILHYV+R+M+ +A
Sbjct: 898 RHGGILHYVLRKMIGSA 914
Lambda K H
0.315 0.134 0.390
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: 2452
Number of extensions: 99
Number of successful extensions: 3
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: 919
Length of database: 914
Length adjustment: 43
Effective length of query: 876
Effective length of database: 871
Effective search space: 762996
Effective search space used: 762996
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: 42 (22.0 bits)
S2: 57 (26.6 bits)
Align candidate WP_043529276.1 JH15_RS08095 (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.3332275.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 1454.0 0.0 0 1453.8 0.0 1.0 1 NCBI__GCF_000759345.1:WP_043529276.1
Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000759345.1:WP_043529276.1
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1453.8 0.0 0 0 2 876 .] 19 911 .. 18 911 .. 0.99
Alignments for each domain:
== domain 1 score: 1453.8 bits; conditional E-value: 0
TIGR01341 2 kvyyyslkaleeslekisklpkslrillesvlrnldgskikeedveallkwkkeelkdeeiafkparvvlqdf 74
+++yysl++++e+l++i++lp +l+ille+ lr d+++++ ed++al++w++e+ + +ei ++parv++qdf
NCBI__GCF_000759345.1:WP_043529276.1 19 EYHYYSLPKAAEALGDIQRLPVTLKILLENQLRFADDESVSREDMQALVDWQQEARSTREIGYRPARVLMQDF 91
79*********************************************************************** PP
TIGR01341 75 tGvpavvdlaalreavknlgkdpekinplvpvdlvidhsvqvdkageeealeanvelefernkerykflkwak 147
tGvp vvdla++r av++lg+dp++inpl+pvdlvidhsv vdk+g+ +a++ nv +e++rn+ery+fl+w++
NCBI__GCF_000759345.1:WP_043529276.1 92 TGVPGVVDLASMRAAVEKLGEDPSRINPLSPVDLVIDHSVMVDKYGDPSAFRDNVAIEMDRNRERYEFLRWGQ 164
************************************************************************* PP
TIGR01341 148 kafknlkvvppgtGivhqvnleylakvvfeaekdgellaypdslvGtdshttminGlGvlGwGvGGieaeaal 220
+af n++vvppgtGi+hqvnleyl+k v+ +e+dg+ +aypd+lvGtdshttminGlGvlGwGvGGieaeaa+
NCBI__GCF_000759345.1:WP_043529276.1 165 DAFDNFRVVPPGTGICHQVNLEYLGKTVWVKEEDGKSFAYPDTLVGTDSHTTMINGLGVLGWGVGGIEAEAAM 237
************************************************************************* PP
TIGR01341 221 lGqpvslsvpeviGvkltGklreGvtatdlvltvtellrkkgvvgkfveffGeglkelsladratianmapey 293
lGqpvs+ +pev+G+kltGklreG+tatdlvltvt++lr+kgvvgkfvef+G+gl+ l+ladratianmapey
NCBI__GCF_000759345.1:WP_043529276.1 238 LGQPVSMLIPEVVGFKLTGKLREGITATDLVLTVTQMLRQKGVVGKFVEFYGDGLDDLPLADRATIANMAPEY 310
************************************************************************* PP
TIGR01341 294 GataaffpiddvtlqylrltgrdedkvelvekylkaqelfvddseepkytdvveldlsdveasvaGpkrpqdr 366
Gat++ffp+dd+tl+ylrltgr++++v lve+y+k q+l+++ ++ep+++d+++ld+ dveas+aGpkrpqdr
NCBI__GCF_000759345.1:WP_043529276.1 311 GATCGFFPVDDETLNYLRLTGRSDEEVALVEAYCKEQDLWRKPGAEPVFSDTLQLDMGDVEASLAGPKRPQDR 383
************************************************************************* PP
TIGR01341 367 valkevkaafksslesnagekglalr....................keakekklegkeaelkdgavviaaits 419
val+++k++f++ + ++a+e + + r + +++ +eg++ +l+ gavviaaits
NCBI__GCF_000759345.1:WP_043529276.1 384 VALSDMKSTFENLMGDDAAEASATARgkfdseggqmpvgthehfehHDSQDVDVEGSTFKLNPGAVVIAAITS 456
*************9999999888887889999999*****999998889999999****************** PP
TIGR01341 420 ctntsnpsvllgagllakkavelGlkvkpyvktslapGskvvtdylaesgllpyleelGfnlvGyGcttciGn 492
ctntsnpsv+++aglla+kave Gl kp+vktslapGskvvtdyla g+++ l++lGfnlvGyGcttciGn
NCBI__GCF_000759345.1:WP_043529276.1 457 CTNTSNPSVMMAAGLLARKAVEKGLDTKPWVKTSLAPGSKVVTDYLAAGGFQDDLNALGFNLVGYGCTTCIGN 529
************************************************************************* PP
TIGR01341 493 sGpleeeveeaikendlevsavlsGnrnfegrihplvkanylaspplvvayalaGtvdidlekepigtdkdGk 565
sGpl +e+ai ++dl+v++vlsGnrnfegr+hplvk+n+laspplvvayalaG+v +d++kep+g +kdGk
NCBI__GCF_000759345.1:WP_043529276.1 530 SGPLLPPIEKAIEDGDLTVASVLSGNRNFEGRVHPLVKTNWLASPPLVVAYALAGNVRLDISKEPLGEGKDGK 602
************************************************************************* PP
TIGR01341 566 kvylkdiwpsakeiaelvkkavkkelfkkeyeevtegnerwnelevtssdlyewdekstyireppffeelkle 638
+vyl+diwps+ eiae+v ++v++e+++key+ev+eg+e w+ ++v++s++y+w e+styi++ppffe++ e
NCBI__GCF_000759345.1:WP_043529276.1 603 PVYLQDIWPSQAEIAEAV-EKVRTEMYRKEYAEVFEGDEVWKAIDVPQSQVYQWSEDSTYIQHPPFFEGMGRE 674
****************65.689*************************************************** PP
TIGR01341 639 peevedikgarillllGdsittdhispaGsikkdspaakylkekGverrdfnsyGsrrGnhevmlrGtfanir 711
pe ++d+++ar+l++lGds+ttdhispaG+ik+dspa++yl+e+Gv++ dfnsyGsrrGnhevm+rGtfan+r
NCBI__GCF_000759345.1:WP_043529276.1 675 PEPLQDVENARVLAMLGDSVTTDHISPAGAIKPDSPAGRYLQEHGVKPMDFNSYGSRRGNHEVMMRGTFANVR 747
************************************************************************* PP
TIGR01341 712 iknklvkgkeGgltvylpdsevvsvydaamkykkegvplvvlaGkeyGsGssrdwaakgtkllGvkaviaesf 784
i+n++++g eGg+t+++p +e++++ydaamky +eg+plvv+aGkeyG+Gssrdwaakgt+llGv+av+aes+
NCBI__GCF_000759345.1:WP_043529276.1 748 IRNEMLDGVEGGYTRHVPSDEQMAIYDAAMKYAEEGRPLVVIAGKEYGTGSSRDWAAKGTRLLGVRAVLAESY 820
************************************************************************* PP
TIGR01341 785 erihrsnlvgmGvlplefkqgedaetlgltgeetidvddieelkpkkevtvelvkedgeketveavlridtev 857
erihrsnl+gmGv+pl+f++ged+++lgltg+e++ +d+i +l p+ +v+v++ +++gek+ +ea +ridt+
NCBI__GCF_000759345.1:WP_043529276.1 821 ERIHRSNLIGMGVVPLQFPEGEDRKSLGLTGDEEVSIDGIADLTPGGQVNVTIKSDKGEKK-IEALCRIDTAN 892
*********************************************************9985.89********* PP
TIGR01341 858 elayvkkgGilqyvlrkll 876
el+y+++gGil+yvlrk++
NCBI__GCF_000759345.1:WP_043529276.1 893 ELEYYRHGGILHYVLRKMI 911
*****************96 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (876 nodes)
Target sequences: 1 (914 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 34.79
//
[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