Align aconitate hydratase (EC 4.2.1.3) (characterized)
to candidate BPHYT_RS33980 BPHYT_RS33980 aconitate hydratase
Query= BRENDA::A0A090AMG4
(901 letters)
>FitnessBrowser__BFirm:BPHYT_RS33980
Length = 905
Score = 1413 bits (3658), Expect = 0.0
Identities = 710/906 (78%), Positives = 786/906 (86%), Gaps = 6/906 (0%)
Query: 1 MPHNTLDTLKNFKIGNKSCQYYSLPALGKSLGIDVQRLPVSIRIVLESVLRNCDGKKVTE 60
M HN TLK F G+ ++YSLP LGK+L I + RLPVSIRIVLESVLRN DGKK+ E
Sbjct: 1 MAHNLHKTLKEFDSGSGKGKFYSLPQLGKALNIKIDRLPVSIRIVLESVLRNYDGKKIAE 60
Query: 61 EHVKQLANWQANARREDEIPFVVARVVLQDFTGVPLLADIAAMRSVADKMGKSPKSIEPL 120
EH++QLANW+ A R DEIPFVV+RVVLQDFTGVPLLADIAAMR VA MGK PKSIEPL
Sbjct: 61 EHIEQLANWKPTAARVDEIPFVVSRVVLQDFTGVPLLADIAAMRGVAKHMGKDPKSIEPL 120
Query: 121 VPVDLVVDHSVMIDYFGTKNALDLNMKLEFKRNQERYQFMKWGMQAFDTFGVVPPGFGIV 180
VPVDLVVDHSV ID+F KNALDLNMKLEF+RN ERYQFMKWGMQAFDTF VVPPG GIV
Sbjct: 121 VPVDLVVDHSVQIDHFREKNALDLNMKLEFQRNNERYQFMKWGMQAFDTFKVVPPGVGIV 180
Query: 181 HQVNLEYLARGVH--LDKKNNVYYPDSLVGTDSHTTMINGIGVVGWGVGGIEAEAGMLGQ 238
HQVNLEYLARGVH + + VYYPDSLVGTDSHTTMINGIGVVGWGVGGIEAEAGMLGQ
Sbjct: 181 HQVNLEYLARGVHKKAEGADTVYYPDSLVGTDSHTTMINGIGVVGWGVGGIEAEAGMLGQ 240
Query: 239 PVYFLTPDVVGVELKGQLRGGVTATDLVLTITEMLRREKVVGKFVEFCGEGTASLSVAER 298
PVYFLTPDVVGVELKG+LR G+TATDLVLT+TE+LR+EKVVGKFVEF GEGT SLS+ +R
Sbjct: 241 PVYFLTPDVVGVELKGKLREGLTATDLVLTVTELLRKEKVVGKFVEFFGEGTKSLSLPDR 300
Query: 299 ATIGNMAPEYGATMGFFPVDERTIDYFRGTGRTEAEIAAFEAYFKAQKMFGVPKAADINF 358
ATIGNMAPEYGATMGFFPVDE+TI+YF+GTGRT+AEI+AFE YFKAQ +FG+PKA I++
Sbjct: 301 ATIGNMAPEYGATMGFFPVDEKTIEYFKGTGRTDAEISAFENYFKAQGLFGIPKAGQIDY 360
Query: 359 TKLLTLDLSTVAPSLAGPKRPQDRIEIGNVKNTFIDLYSKPVAENGFNQPAEKLAQTFTT 418
TK++TLDL TV PSLAGPKRPQDRIEIG+VK+TF DL+SKPVAENGF + A L +TT
Sbjct: 361 TKVVTLDLGTVTPSLAGPKRPQDRIEIGHVKSTFSDLFSKPVAENGFAKKAADLEAQYTT 420
Query: 419 SAGTQVKNGDILIAAITSCTNTSNPSVLLAAGLLAKKAVEAGLTVPKHIKTSLAPGSRVV 478
S G VKNGDILIAAITSCTNTSNPSVLLAAGLLAKKAVEAGLTV HIKTSLAPGSR+V
Sbjct: 421 SNGVDVKNGDILIAAITSCTNTSNPSVLLAAGLLAKKAVEAGLTVAPHIKTSLAPGSRIV 480
Query: 479 TEYLTKTGLLPYLEKLGFDVAAYGCTTCIGNAGDLTPDLNEAIIGNDLICSAVLSGNRNF 538
TEYLTKT L+ YL+KLGF +AAYGCTTCIGNAGDLTP+LNEAI ND++ +AVLSGNRNF
Sbjct: 481 TEYLTKTDLMKYLDKLGFTLAAYGCTTCIGNAGDLTPELNEAITKNDIVAAAVLSGNRNF 540
Query: 539 EARIHPNIKANFLASPPLVVAYALAGTVTRDLMTEPVGRGKNG-DVWLGDIWPTTEEIES 597
EARIHPNI+ANFLASPPLVVAYA+AG +TRDLMTEPVG+GK G D++LGDIWPT+EE+
Sbjct: 541 EARIHPNIRANFLASPPLVVAYAIAGNITRDLMTEPVGKGKGGKDIYLGDIWPTSEEVNE 600
Query: 598 LLKYALDPKAFEANYGQVKSNPGKLWENTKGVTGDTYNWPDSTYIAEPPFF-EGFGMTPG 656
LLK+ALD AF NY + + G LW +G G Y+WP STYIAEPPFF + F M P
Sbjct: 601 LLKFALDADAFRKNYSAL-TKKGDLWSKIEGEEGQVYDWPKSTYIAEPPFFGKDFSMQPA 659
Query: 657 -AMPAVKGARALGVFGDSVTTDHISPAGSIKETSPAGKWLKENGVMKADFNSYGSRRGNH 715
++ AVK ARALG+FGDSVTTDHISPAGSIKE SPAGKWLKENGV KADFNSYGSRRGNH
Sbjct: 660 DSIAAVKDARALGIFGDSVTTDHISPAGSIKEDSPAGKWLKENGVQKADFNSYGSRRGNH 719
Query: 716 EIMMRGTFANVRIKNLMIPALPDGSRFEGGETLFQPTGEQMSIYDAAMKYVSAGTPTVVF 775
++MMRGTFANVRIKNLMIPA DG+R EGG T+ QP+GEQ+SIYDAAMKY+ AGTPTVVF
Sbjct: 720 DVMMRGTFANVRIKNLMIPAKADGTRVEGGLTIHQPSGEQLSIYDAAMKYIDAGTPTVVF 779
Query: 776 GGEEYGTGSSRDWAAKGTQLLGVKAVITRSFERIHRSNLVGMGVLPLQFKGADSVQSLGI 835
GEEYGTGSSRDWAAKGTQLLGVK V+ RSFERIHRSNLVGMGVLPLQFKG+DSVQSLGI
Sbjct: 780 AGEEYGTGSSRDWAAKGTQLLGVKVVVARSFERIHRSNLVGMGVLPLQFKGSDSVQSLGI 839
Query: 836 TGEETYDISGLEDGIKPMQDVTLTITRKDGSKQDVTVLLRIDTPIEVDYYQHGGILPFVL 895
TGEETYDI GL KP Q+VTL I K+G ++ V VLLRIDTPIEVDYY+HGGILPFVL
Sbjct: 840 TGEETYDIEGLGADFKPQQEVTLVIRDKEGKEKRVQVLLRIDTPIEVDYYKHGGILPFVL 899
Query: 896 RQLLAA 901
R LLAA
Sbjct: 900 RSLLAA 905
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: 2397
Number of extensions: 102
Number of successful extensions: 5
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: 905
Length adjustment: 43
Effective length of query: 858
Effective length of database: 862
Effective search space: 739596
Effective search space used: 739596
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 BPHYT_RS33980 BPHYT_RS33980 (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.8136.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 1319.3 0.0 0 1319.1 0.0 1.0 1 lcl|FitnessBrowser__BFirm:BPHYT_RS33980 BPHYT_RS33980 aconitate hydratas
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__BFirm:BPHYT_RS33980 BPHYT_RS33980 aconitate hydratase
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1319.1 0.0 0 0 3 876 .] 19 903 .. 17 903 .. 0.97
Alignments for each domain:
== domain 1 score: 1319.1 bits; conditional E-value: 0
TIGR01341 3 vyyyslkalees.lekisklpkslrillesvlrnldgskikeedveallkwkkeelkdeeiafkparvvl 71
++ysl++l ++ + ki++lp s+ri+lesvlrn dg+ki ee++e+l++wk ++ + ei+f ++rvvl
lcl|FitnessBrowser__BFirm:BPHYT_RS33980 19 GKFYSLPQLGKAlNIKIDRLPVSIRIVLESVLRNYDGKKIAEEHIEQLANWKPTAARVDEIPFVVSRVVL 88
579******998788******************************************************* PP
TIGR01341 72 qdftGvpavvdlaalreavknlgkdpekinplvpvdlvidhsvqvdkageeealeanvelefernkeryk 141
qdftGvp++ d+aa+r k++gkdp+ i+plvpvdlv+dhsvq+d+++e++al+ n++lef+rn+ery+
lcl|FitnessBrowser__BFirm:BPHYT_RS33980 89 QDFTGVPLLADIAAMRGVAKHMGKDPKSIEPLVPVDLVVDHSVQIDHFREKNALDLNMKLEFQRNNERYQ 158
********************************************************************** PP
TIGR01341 142 flkwakkafknlkvvppgtGivhqvnleylakvvfeaekdgellaypdslvGtdshttminGlGvlGwGv 211
f+kw+ +af +kvvppg Givhqvnleyla+ v+++ + +++ ypdslvGtdshttminG+Gv+GwGv
lcl|FitnessBrowser__BFirm:BPHYT_RS33980 159 FMKWGMQAFDTFKVVPPGVGIVHQVNLEYLARGVHKKAEGADTVYYPDSLVGTDSHTTMINGIGVVGWGV 228
**************************************99999*************************** PP
TIGR01341 212 GGieaeaallGqpvslsvpeviGvkltGklreGvtatdlvltvtellrkkgvvgkfveffGeglkelsla 281
GGieaea++lGqpv++ p+v+Gv l+GklreG+tatdlvltvtellrk+ vvgkfveffGeg k+lsl+
lcl|FitnessBrowser__BFirm:BPHYT_RS33980 229 GGIEAEAGMLGQPVYFLTPDVVGVELKGKLREGLTATDLVLTVTELLRKEKVVGKFVEFFGEGTKSLSLP 298
********************************************************************** PP
TIGR01341 282 dratianmapeyGataaffpiddvtlqylrltgrdedkvelvekylkaqelfvd.dseepkytdvveldl 350
drati nmapeyGat++ffp+d++t++y++ tgr + +++ e+y kaq+lf ++ ++ yt+vv ldl
lcl|FitnessBrowser__BFirm:BPHYT_RS33980 299 DRATIGNMAPEYGATMGFFPVDEKTIEYFKGTGRTDAEISAFENYFKAQGLFGIpKAGQIDYTKVVTLDL 368
****************************************************988999************ PP
TIGR01341 351 sdveasvaGpkrpqdrvalkevkaafksslesnagekglalrkeakekkle.gkeaelkdgavviaaits 419
+v +s+aGpkrpqdr+++ +vk++f ++++++e+g+a + e + + +k+g++ iaaits
lcl|FitnessBrowser__BFirm:BPHYT_RS33980 369 GTVTPSLAGPKRPQDRIEIGHVKSTFSDLFSKPVAENGFAKKAADLEAQYTtSNGVDVKNGDILIAAITS 438
**************************************9988666555443278899************* PP
TIGR01341 420 ctntsnpsvllgagllakkavelGlkvkpyvktslapGskvvtdylaesgllpyleelGfnlvGyGcttc 489
ctntsnpsvll+agllakkave+Gl v p++ktslapGs++vt+yl++++l++yl++lGf+l yGcttc
lcl|FitnessBrowser__BFirm:BPHYT_RS33980 439 CTNTSNPSVLLAAGLLAKKAVEAGLTVAPHIKTSLAPGSRIVTEYLTKTDLMKYLDKLGFTLAAYGCTTC 508
********************************************************************** PP
TIGR01341 490 iGnsGpleeeveeaikendlevsavlsGnrnfegrihplvkanylaspplvvayalaGtvdidlekepig 559
iGn+G+l+ e++eai++nd++++avlsGnrnfe+rihp ++an+laspplvvaya+aG+++ dl +ep+g
lcl|FitnessBrowser__BFirm:BPHYT_RS33980 509 IGNAGDLTPELNEAITKNDIVAAAVLSGNRNFEARIHPNIRANFLASPPLVVAYAIAGNITRDLMTEPVG 578
********************************************************************** PP
TIGR01341 560 tdkdGkkvylkdiwpsakeiaelvkkavkkelfkkeyeevtegnerwnelevtssdlyewdekstyirep 629
+k Gk++yl diwp+ +e++el k a+ + f+k+y+++t++ + w ++e ++++y+w +kstyi ep
lcl|FitnessBrowser__BFirm:BPHYT_RS33980 579 KGKGGKDIYLGDIWPTSEEVNELLKFALDADAFRKNYSALTKKGDLWSKIEGEEGQVYDW-PKSTYIAEP 647
************************************************************.79******* PP
TIGR01341 630 pff.eelklepee.vedikgarillllGdsittdhispaGsikkdspaakylkekGverrdfnsyGsrrG 697
pff ++++++p++ + +k+ar l +Gds+ttdhispaGsik+dspa+k+lke+Gv++ dfnsyGsrrG
lcl|FitnessBrowser__BFirm:BPHYT_RS33980 648 PFFgKDFSMQPADsIAAVKDARALGIFGDSVTTDHISPAGSIKEDSPAGKWLKENGVQKADFNSYGSRRG 717
***66899999762678***************************************************** PP
TIGR01341 698 nhevmlrGtfaniriknklvkgk......eGgltvylpdsevvsvydaamkykkegvplvvlaGkeyGsG 761
nh+vm+rGtfan+rikn ++++k eGglt++ p +e++s+ydaamky + g+p+vv aG+eyG+G
lcl|FitnessBrowser__BFirm:BPHYT_RS33980 718 NHDVMMRGTFANVRIKNLMIPAKadgtrvEGGLTIHQPSGEQLSIYDAAMKYIDAGTPTVVFAGEEYGTG 787
*******************98643333448**************************************** PP
TIGR01341 762 ssrdwaakgtkllGvkaviaesferihrsnlvgmGvlplefkqgedaetlgltgeetidvddi.eelkpk 830
ssrdwaakgt+llGvk+v+a+sferihrsnlvgmGvlpl+fk ++ ++lg+tgeet d++++ + kp+
lcl|FitnessBrowser__BFirm:BPHYT_RS33980 788 SSRDWAAKGTQLLGVKVVVARSFERIHRSNLVGMGVLPLQFKGSDSVQSLGITGEETYDIEGLgADFKPQ 857
**************************************************************7369**** PP
TIGR01341 831 kevtvelvkedgeketveavlridtevelayvkkgGilqyvlrkll 876
+evt+++ +++g+++ v++ lridt++e++y+k+gGil +vlr ll
lcl|FitnessBrowser__BFirm:BPHYT_RS33980 858 QEVTLVIRDKEGKEKRVQVLLRIDTPIEVDYYKHGGILPFVLRSLL 903
******************************************9876 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (876 nodes)
Target sequences: 1 (905 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: 0.04u 0.02s 00:00:00.06 Elapsed: 00:00:00.06
# Mc/sec: 12.25
//
[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