Align Aconitate hydratase, mitochondrial; Aconitase; Citrate hydro-lyase; EC 4.2.1.3 (characterized)
to candidate WP_022947288.1 H035_RS0101725 aconitate hydratase
Query= SwissProt::P16276
(781 letters)
>NCBI__GCF_000421465.1:WP_022947288.1
Length = 652
Score = 312 bits (800), Expect = 3e-89
Identities = 236/719 (32%), Positives = 350/719 (48%), Gaps = 85/719 (11%)
Query: 64 TLSEKIVYGHLDDPANQEIERGKTYLRLRPDRVAMQDATAQMAMLQFISSGLPKVAVP-S 122
++++K++ HL +E G+ + L+ D+ QDAT + ML+F + G+P+V S
Sbjct: 4 SVAQKLIESHL---VEGRMEAGEE-IGLKIDQTLTQDATGTLVMLEFEALGVPRVRTELS 59
Query: 123 TIHCDHLIEAQLGGEKDLRRAKDINQEVYNFLATAGAKYGVGFWRPGSGIIHQIILENYA 182
+ DH + ++D + D + FL +A K+G+ F RPG+G+ H + +E +
Sbjct: 60 AQYVDHNLL-----QEDFKNPDD-----HLFLRSACKKFGLWFSRPGNGVSHPVHMERFG 109
Query: 183 YPGVLLIGTDSHTPNGGGLGGICIGVGGADAVDVMAGIPWELKCPKVIGVKLTGSLSGWT 242
PG L+G+DSHT G LG + IG GG + MAG P+ L+ PK+ GV+LTG L W
Sbjct: 110 IPGKTLLGSDSHTCAAGSLGMLAIGAGGLEVTMAMAGEPFHLRMPKIWGVRLTGRLPDWV 169
Query: 243 SPKDVILKVAGILTVKGGTGAIVEYHGPGVDSISCTGMATICNMGAEIGATTSVFPYNHR 302
S KDVIL++ V GG G IVEY+GPG+D ++ I NMGAE+GATT+VFP +
Sbjct: 170 SAKDVILEMLRRHGVDGGLGKIVEYYGPGLDHLTAMDRHVIANMGAELGATTTVFPADDA 229
Query: 303 MKKYLSKTGRADIANLADEFKDHLVPDPGCHYDQVIEINLSELKPHINGPFTPDLAHPVA 362
++ +L+ GR D ++ DP YD+ EI+LS+L+P I P +P PV+
Sbjct: 230 VRTFLTTQGRGDAWR-------EMLADPDARYDEHDEIDLSQLEPLIALPSSPGHVVPVS 282
Query: 363 EVGSVAEKEGWPLDIRVGLIGSCTNSSYEDMGRSAAVAKQALAHGLKCKSQFTITPGSEQ 422
EV +I IGS N D +AA+ H + F + P S Q
Sbjct: 283 EVAG--------REIYQSYIGSSANPGLRDFAVAAAIVDGKQVHD---RVSFDVNPTSRQ 331
Query: 423 IRATIERDGYAQVLRDVGGIVLANACGPCIGQWDRKDIKKGEKNTIVTSYNRNFTGRNDA 482
I + G + L G + CG CIG + T+ RNF GR+
Sbjct: 332 ILENMVELGILKKLIHAGARLHQAGCGGCIGMGQAPASGRISLRTV----PRNFPGRS-G 386
Query: 483 NPETHAFVTSPEIVTALAIAGTLKFNPETDFLTGKDGKKFKLEAPDADELPRAEFDPGQD 542
E ++ SPE A A+ G + D + + P E PR +
Sbjct: 387 TKEDQVYLCSPETAAASALTGVI-----------TDPRTLDMPYPRFRE-PRTLLINTEM 434
Query: 543 TYQHPPKDSSGQRVDVSPTSQRLQLLEPF-DKWDGKDLEDLQILIKVKGKCTTDHISAAG 601
P+D +G +++ P Q L L+P +K +G +L+KV +TD I AG
Sbjct: 435 LVPPAPQD-AGVELEMGPNIQPLPALDPLPEKLEG------PVLLKVADNISTDEILPAG 487
Query: 602 -PWLKFRGHLDNISNNLLIGAINIENRKANSVRNAVTQEFGPVPDTARYYKQHGIRWVVI 660
L FR ++ IS V N V + + + A +Q G ++
Sbjct: 488 AKVLPFRSNIPEIS---------------KFVFNPVDESY---YERAMASRQQGS--FIV 527
Query: 661 GDENYGEGSSREHRALEPRHLGGRAIITKSFARIHETNLKKQGLLPLTFADPADYNKIHP 720
G NYG+GSSREH AL PR+LG RA+I KSFARIH NL G+LPLT D D+ KI
Sbjct: 528 GGVNYGQGSSREHAALAPRYLGLRAVIAKSFARIHRQNLSNFGILPLTLVDAEDWEKIAQ 587
Query: 721 VDKLTIQGLKD-FAPGKPLKCIIKHPNGTQ-ETILLNHTFNETQIEWFRAGSALNRMKE 777
D ++I ++ G ++ I N T+ E + H + Q+E AGS +N ++E
Sbjct: 588 GDVISIPDVRQVLRQGDRVEVI----NRTRDERYVTEHRLSRRQVEMVLAGSLINLVRE 642
Lambda K H
0.318 0.137 0.413
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: 1233
Number of extensions: 53
Number of successful extensions: 7
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: 781
Length of database: 652
Length adjustment: 39
Effective length of query: 742
Effective length of database: 613
Effective search space: 454846
Effective search space used: 454846
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: 55 (25.8 bits)
Align candidate WP_022947288.1 H035_RS0101725 (aconitate hydratase)
to HMM TIGR01342 (putative aconitate hydratase (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/TIGR01342.hmm
# target sequence database: /tmp/gapView.19930.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: TIGR01342 [M=655]
Accession: TIGR01342
Description: acon_putative: putative aconitate hydratase
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
------- ------ ----- ------- ------ ----- ---- -- -------- -----------
2.1e-255 834.9 0.0 2.4e-255 834.7 0.0 1.0 1 lcl|NCBI__GCF_000421465.1:WP_022947288.1 H035_RS0101725 aconitate hydrata
Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000421465.1:WP_022947288.1 H035_RS0101725 aconitate hydratase
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 834.7 0.0 2.4e-255 2.4e-255 2 650 .. 5 645 .. 4 650 .. 0.98
Alignments for each domain:
== domain 1 score: 834.7 bits; conditional E-value: 2.4e-255
TIGR01342 2 laekilddhlvegdlepgeeiaikidqtlsqdatgtmvylefealevdevktelavsyidhqtlqtdfk 70
+a+k+++ hlveg +e geei++kidqtl+qdatgt+v lefeal+v+ v+tel+++y+dh++lq dfk
lcl|NCBI__GCF_000421465.1:WP_022947288.1 5 VAQKLIESHLVEGRMEAGEEIGLKIDQTLTQDATGTLVMLEFEALGVPRVRTELSAQYVDHNLLQEDFK 73
899****************************************************************** PP
TIGR01342 71 naddhkylrsvakkygiylskpgngichqvhkerfakpgktllgsdshtptagglgqlaigaggldvav 139
n ddh +lrs+ kk+g+++s+pgng+ h vh+erf pgktllgsdsht +ag lg+laigaggl+v++
lcl|NCBI__GCF_000421465.1:WP_022947288.1 74 NPDDHLFLRSACKKFGLWFSRPGNGVSHPVHMERFGIPGKTLLGSDSHTCAAGSLGMLAIGAGGLEVTM 142
********************************************************************* PP
TIGR01342 140 amageayylkmpkvvnvrlkgklpewvtakdvilellrrlsvkgglgkvleytgegvkelsvperatit 208
amage+++l+mpk+ +vrl g+lp+wv+akdvile+lrr v gglgk++ey+g+g+++l+ +r i+
lcl|NCBI__GCF_000421465.1:WP_022947288.1 143 AMAGEPFHLRMPKIWGVRLTGRLPDWVSAKDVILEMLRRHGVDGGLGKIVEYYGPGLDHLTAMDRHVIA 211
********************************************************************* PP
TIGR01342 209 nmgaelgatssifpsdeitedylaafdreeefvelladadaeydevivvdlselepliaepsspdnvvp 277
nmgaelgat+++fp+d+ + +l++++r + + e+lad+da yde ++dls+leplia pssp vvp
lcl|NCBI__GCF_000421465.1:WP_022947288.1 212 NMGAELGATTTVFPADDAVRTFLTTQGRGDAWREMLADPDARYDEHDEIDLSQLEPLIALPSSPGHVVP 280
********************************************************************* PP
TIGR01342 278 vrevegikveqvvvgsctnsayvdllraakllegrevskdvvlivapgskqalellaregallellkag 346
v ev+g ++ q +gs +n d aa +++g++v++ v + v p s+q le + + g l +l++ag
lcl|NCBI__GCF_000421465.1:WP_022947288.1 281 VSEVAGREIYQSYIGSSANPGLRDFAVAAAIVDGKQVHDRVSFDVNPTSRQILENMVELGILKKLIHAG 349
********************************************************************* PP
TIGR01342 347 vrileaacgacigigfvpasdsvslrsfnrnfkgragieddkvylaspevavaaaiageivdprdlaed 415
+r+ +a cg cig+g +pas +slr+ rnf gr+g+++d+vyl+spe+a+a+a++g i dpr l
lcl|NCBI__GCF_000421465.1:WP_022947288.1 350 ARLHQAGCGGCIGMGQAPASGRISLRTVPRNFPGRSGTKEDQVYLCSPETAAASALTGVITDPRTLD-- 416
****************************************************************985.. PP
TIGR01342 416 eglkairvemgekysygdeadidiltkeeridvelikgpnikslpvkeplgedvegevllkvednittd 484
+ ++r+ + e +++ +++ vel gpni++lp +pl+e++eg vllkv dni+td
lcl|NCBI__GCF_000421465.1:WP_022947288.1 417 --MPYPRFREPRTLLINTEMLVPPAPQDA--GVELEMGPNIQPLPALDPLPEKLEGPVLLKVADNISTD 481
..789******************999876..577888******************************** PP
TIGR01342 485 hiipatadilklrsniealseyvlsrvddefverakkldekgkagvlvagenygqgssrehaalaprfl 553
i+pa+a++l++rsni +s++v++ vd+ + era + + + +v+g nygqgssrehaalapr+l
lcl|NCBI__GCF_000421465.1:WP_022947288.1 482 EILPAGAKVLPFRSNIPEISKFVFNPVDESYYERAMASRQ--QGSFIVGGVNYGQGSSREHAALAPRYL 548
**********************************999888..6689*********************** PP
TIGR01342 554 gveavlaksfarihkanlvnfgvlpleidnkedydkielgdevevvdliealkdgeeilvvrktddeei 622
g++av+aksfarih+ nl nfg+lpl + + ed++ki +gd + ++d+ + l++g+ + v+++t de
lcl|NCBI__GCF_000421465.1:WP_022947288.1 549 GLRAVIAKSFARIHRQNLSNFGILPLTLVDAEDWEKIAQGDVISIPDVRQVLRQGDRVEVINRTRDERY 617
********************************************************************* PP
TIGR01342 623 latldlsevekeiliaggklslikqkhr 650
++ + ls ++ e+++ag ++l++++ +
lcl|NCBI__GCF_000421465.1:WP_022947288.1 618 VTEHRLSRRQVEMVLAGSLINLVRERVT 645
***********************99865 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (655 nodes)
Target sequences: 1 (652 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: 0.03u 0.02s 00:00:00.05 Elapsed: 00:00:00.05
# Mc/sec: 7.61
//
[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