Align Aconitate hydratase A; ACN; Aconitase; (2R,3S)-2-methylisocitrate dehydratase; (2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate dehydratase; Iron-responsive protein-like; IRP-like; Probable 2-methyl-cis-aconitate hydratase; RNA-binding protein; EC 4.2.1.3; EC 4.2.1.99 (characterized)
to candidate WP_073036524.1 BUB04_RS02125 aconitate hydratase AcnA
Query= SwissProt::Q5SMF6
(902 letters)
>NCBI__GCF_900129305.1:WP_073036524.1
Length = 881
Score = 994 bits (2571), Expect = 0.0
Identities = 514/881 (58%), Positives = 641/881 (72%), Gaps = 22/881 (2%)
Query: 17 TYGYYDLQELERKGVAEVSRLPFSIRVMLESLLRNEDGYQVTREDIEALARWRPDPGE-I 75
T+ + DL+ L + RLP+SIRV+LE+++R D VT D+E LA WR E +
Sbjct: 13 TFEFVDLKGLFGN---RLGRLPYSIRVLLENVVRRRDDRLVTERDVENLAGWRGRYAEPV 69
Query: 76 NVPLKLARVILQDFTGVPAVVDLAAMRDAIKAKGGDPKRINPVVPADLVIDHSVQVDAFG 135
+P ARV++QDFTGVPAV DLAAMRDA+ A G DP +NP+VP DLV+DHSVQVD FG
Sbjct: 70 EIPFFPARVLMQDFTGVPAVADLAAMRDALVALGKDPAAVNPLVPVDLVVDHSVQVDFFG 129
Query: 136 TAYAFFYNVEKEYERNRERYLLLKWAQNALENFRVVPPGTGIVHQVNIEYLTKVVMTGKR 195
T+ A NV +EYERN ERY LKWAQ + ENFRVVPP +GI HQVN+E+L++V K
Sbjct: 130 TSDALTANVRREYERNGERYTFLKWAQKSFENFRVVPPNSGICHQVNLEHLSRVFWDRKE 189
Query: 196 DGLTLAFPDSLVGTDSHTTMVNGLGVLGWGVGGIEAEAVMLGQPYYMLAPRVVGFKLYGE 255
DG+ + FPD++VG DSHTTMVNG+GVLGWGVGGIEAEAV++GQPY M P V+G +L G
Sbjct: 190 DGVRICFPDTVVGLDSHTTMVNGIGVLGWGVGGIEAEAVLMGQPYSMAIPEVIGVRLVGR 249
Query: 256 LPEGATATDLVLTVTEMLRKHGVVGKFVEFYGPGVAKLSTPDRATIANMAPEYGATMGFF 315
LP A ATDLVL VTE LR +GVV KFVEF+GP V LS P RATIANM+PEYGAT+GFF
Sbjct: 250 LPRRANATDLVLRVTEALRDYGVVEKFVEFFGPAVTALSVPARATIANMSPEYGATVGFF 309
Query: 316 PVDEETLNYLRQTGRPEELVELVEAYTKAVGLFRTPEAEEKVQYSEYLELDLSAVEPSLA 375
PVDE+ + YLR T R E + EA +A+GL+ + E+ Y++ LE+DLSA+ P++A
Sbjct: 310 PVDEKVVEYLRLTHR-ERQARVTEAAARAMGLYY--DGSEEPDYTDVLEIDLSAIRPAVA 366
Query: 376 GPKRPQDRVPLKEVKKSFLAHLTKPVKERGFGLSEDQLQRKVLVKRRDEEFELTHGSVVI 435
GP +P+DR+ L E+K F + RG ED + V V+ R E EL+ GSVVI
Sbjct: 367 GPSKPKDRIELSELKTRFR-------QLRG----EDAPKAAVPVRIRGENVELSDGSVVI 415
Query: 436 AAITSCTNTSNPSVMLGAGLLAKKAVEAGLDRKPWVKTSLAPGSKVVTDYLEMSGLMPFL 495
AAITSCTNTSNP +LGA LLA+ AV+ GL VKTSLAPGSKVV YL+ SGL+P+L
Sbjct: 416 AAITSCTNTSNPHALLGAALLARNAVKRGLAVPAHVKTSLAPGSKVVVQYLDRSGLLPYL 475
Query: 496 EALGFHLVGYGCTTCIGNSGPLPEDIAKAVEEGNLVVAAVLSGNRNFEGRINPHVKANYL 555
EALGFH V +GCTTCIGNSGPL ++ +A+EE NL VAAVLSGNRNFE RI+ VK+N+L
Sbjct: 476 EALGFHPVAFGCTTCIGNSGPLHPEVERAIEEHNLNVAAVLSGNRNFEARIHQKVKSNFL 535
Query: 556 ASPMLVVAYALAGRMDIDFTTEPLGFDPNGKPIYLKDIWPSMEEIREAIRKTLDPELFKK 615
ASP+LVVA+ALAGR+D+D EP+G DPNG P++L DI P EEI E + + + +LF++
Sbjct: 536 ASPLLVVAFALAGRVDVDLEKEPVGLDPNGGPVFLADILPDDEEIEELVNRYVQEDLFRE 595
Query: 616 EYSKVFEGDERWQALPAPTGELYQWDPESTYIQNPPFFEDLGERKVE--DIRGARVLLVL 673
Y K+ EGD+ W L Y WDP STYI+ PP+FE + E DIRGARVLL L
Sbjct: 596 TYEKILEGDQFWNELQVQESVTYPWDPRSTYIKCPPYFEGFTPQMPETTDIRGARVLLWL 655
Query: 674 GDSVTTDHISPAGAIPVKSPAGQYLISKGVKPEDFNSYGSRRGNHEVMMRGTFANIRIKN 733
GD+VTTDHISPAGAI PAG+YL S G+ ++FNSYG+RRGNHEVMMRGTFANIRI+N
Sbjct: 656 GDAVTTDHISPAGAIHEDYPAGRYLKSLGLSRQEFNSYGARRGNHEVMMRGTFANIRIRN 715
Query: 734 LMLDGIEGGYAKKLPEGDVDFVYNVAMRYKAEGTPLLVIAGKEYGTGSSRDWAAKGTYLL 793
++ G + K PEG+ +V+ A Y+ EG PL+V+ GKEYGTGSSRDWAAKG LL
Sbjct: 716 KLVSE-PGSFTVKFPEGERMYVFEAAEAYRREGVPLIVLGGKEYGTGSSRDWAAKGPKLL 774
Query: 794 GIRAVLAESFERIHRSNLVGMGVLPLEFLPGENRETLGLTGYEVYDILGLEDLKPRKLVD 853
G++AV+AESFERIHRSNL+GMG+LPL+FL GE+ E+LGL G E Y I G+ ++PR+ +
Sbjct: 775 GVKAVIAESFERIHRSNLIGMGILPLQFLEGESAESLGLDGTEEYHIAGIAGIEPRRKLT 834
Query: 854 IVARREDGSEVRFQAIARLDTPVEVDYYKNGGILQTVLLNM 894
+ A + DG E FQ +ARLDT +E DYY+NGGIL VL M
Sbjct: 835 VTAVK-DGKEKTFQVLARLDTEIEADYYRNGGILDYVLRKM 874
Lambda K H
0.317 0.137 0.399
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: 2161
Number of extensions: 87
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: 902
Length of database: 881
Length adjustment: 43
Effective length of query: 859
Effective length of database: 838
Effective search space: 719842
Effective search space used: 719842
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 WP_073036524.1 BUB04_RS02125 (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.2697884.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 1290.6 0.0 0 1290.5 0.0 1.0 1 NCBI__GCF_900129305.1:WP_073036524.1
Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900129305.1:WP_073036524.1
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1290.5 0.0 0 0 5 875 .. 16 874 .. 12 875 .. 0.98
Alignments for each domain:
== domain 1 score: 1290.5 bits; conditional E-value: 0
TIGR01341 5 yyslkaleeslekisklpkslrillesvlrnldgskikeedveallkwkkeelkdeeiafkparvvlqdftGv 77
+ lk l+ ++++ +lp+s+r+lle+v+r+ d++ ++e+dve+l+ w+ + +ei+f parv++qdftGv
NCBI__GCF_900129305.1:WP_073036524.1 16 FVDLKGLF--GNRLGRLPYSIRVLLENVVRRRDDRLVTERDVENLAGWRGRYAEPVEIPFFPARVLMQDFTGV 86
55667777..88999********************************************************** PP
TIGR01341 78 pavvdlaalreavknlgkdpekinplvpvdlvidhsvqvdkageeealeanvelefernkerykflkwakkaf 150
pav dlaa+r+a+ +lgkdp+ +nplvpvdlv+dhsvqvd +g+++al anv++e+ern ery+flkwa+k+f
NCBI__GCF_900129305.1:WP_073036524.1 87 PAVADLAAMRDALVALGKDPAAVNPLVPVDLVVDHSVQVDFFGTSDALTANVRREYERNGERYTFLKWAQKSF 159
************************************************************************* PP
TIGR01341 151 knlkvvppgtGivhqvnleylakvvfeaekdgellaypdslvGtdshttminGlGvlGwGvGGieaeaallGq 223
+n++vvpp +Gi+hqvnle+l++v ++ ++dg + +pd++vG dshttm+nG+GvlGwGvGGieaea+l+Gq
NCBI__GCF_900129305.1:WP_073036524.1 160 ENFRVVPPNSGICHQVNLEHLSRVFWDRKEDGVRICFPDTVVGLDSHTTMVNGIGVLGWGVGGIEAEAVLMGQ 232
************************************************************************* PP
TIGR01341 224 pvslsvpeviGvkltGklreGvtatdlvltvtellrkkgvvgkfveffGeglkelsladratianmapeyGat 296
p+s+++peviGv+l+G+l atdlvl+vte lr+ gvv+kfveffG++++ ls++ ratianm+peyGat
NCBI__GCF_900129305.1:WP_073036524.1 233 PYSMAIPEVIGVRLVGRLPRRANATDLVLRVTEALRDYGVVEKFVEFFGPAVTALSVPARATIANMSPEYGAT 305
************************************************************************* PP
TIGR01341 297 aaffpiddvtlqylrltgrdedkvelvekylkaqelfvddseepkytdvveldlsdveasvaGpkrpqdrval 369
++ffp+d++ ++ylrlt r+ + + e+ ++a +l++d seep ytdv+e+dls ++++vaGp +p+dr++l
NCBI__GCF_900129305.1:WP_073036524.1 306 VGFFPVDEKVVEYLRLTHRER-QARVTEAAARAMGLYYDGSEEPDYTDVLEIDLSAIRPAVAGPSKPKDRIEL 377
*******************99.899************************************************ PP
TIGR01341 370 kevkaafksslesnagekglalrkeakekklegkeaelkdgavviaaitsctntsnpsvllgagllakkavel 442
+e+k+ f++ ++a +k a+ + g++ el+dg+vviaaitsctntsnp llga+lla+ av+
NCBI__GCF_900129305.1:WP_073036524.1 378 SELKTRFRQLRGEDA-------PKAAVPVRIRGENVELSDGSVVIAAITSCTNTSNPHALLGAALLARNAVKR 443
*****9986543333.......5667778889***************************************** PP
TIGR01341 443 GlkvkpyvktslapGskvvtdylaesgllpyleelGfnlvGyGcttciGnsGpleeeveeaikendlevsavl 515
Gl v+ +vktslapGskvv +yl +sgllpyle+lGf+ v +GcttciGnsGpl+ eve ai e +l+v+avl
NCBI__GCF_900129305.1:WP_073036524.1 444 GLAVPAHVKTSLAPGSKVVVQYLDRSGLLPYLEALGFHPVAFGCTTCIGNSGPLHPEVERAIEEHNLNVAAVL 516
************************************************************************* PP
TIGR01341 516 sGnrnfegrihplvkanylaspplvvayalaGtvdidlekepigtdkdGkkvylkdiwpsakeiaelvkkavk 588
sGnrnfe+rih+ vk+n+lasp lvva+alaG+vd+dlekep+g d +G +v+l di p +ei+elv+++v+
NCBI__GCF_900129305.1:WP_073036524.1 517 SGNRNFEARIHQKVKSNFLASPLLVVAFALAGRVDVDLEKEPVGLDPNGGPVFLADILPDDEEIEELVNRYVQ 589
************************************************************************* PP
TIGR01341 589 kelfkkeyeevtegnerwnelevtssdlyewdekstyireppffeelklepeevedikgarillllGdsittd 661
++lf+++ye++ eg++ wnel+v +s +y wd++styi+ pp+fe+++ + e +di+gar+ll lGd +ttd
NCBI__GCF_900129305.1:WP_073036524.1 590 EDLFRETYEKILEGDQFWNELQVQESVTYPWDPRSTYIKCPPYFEGFTPQMPETTDIRGARVLLWLGDAVTTD 662
************************************************************************* PP
TIGR01341 662 hispaGsikkdspaakylkekGverrdfnsyGsrrGnhevmlrGtfaniriknklvkgkeGgltvylpdsevv 734
hispaG+i++d pa++ylk G++r++fnsyG+rrGnhevm+rGtfaniri+nklv + G++tv +p++e +
NCBI__GCF_900129305.1:WP_073036524.1 663 HISPAGAIHEDYPAGRYLKSLGLSRQEFNSYGARRGNHEVMMRGTFANIRIRNKLVS-EPGSFTVKFPEGERM 734
********************************************************9.9************** PP
TIGR01341 735 svydaamkykkegvplvvlaGkeyGsGssrdwaakgtkllGvkaviaesferihrsnlvgmGvlplefkqged 807
v++aa y++egvpl+vl GkeyG+Gssrdwaakg+kllGvkaviaesferihrsnl+gmG+lpl+f +ge+
NCBI__GCF_900129305.1:WP_073036524.1 735 YVFEAAEAYRREGVPLIVLGGKEYGTGSSRDWAAKGPKLLGVKAVIAESFERIHRSNLIGMGILPLQFLEGES 807
************************************************************************* PP
TIGR01341 808 aetlgltgeetidvddieelkpkkevtvelvkedgeketveavlridtevelayvkkgGilqyvlrkl 875
ae+lgl+g+e+ ++ +i ++p++++tv++vk dg+++t+++ +r+dte+e +y+++gGil+yvlrk+
NCBI__GCF_900129305.1:WP_073036524.1 808 AESLGLDGTEEYHIAGIAGIEPRRKLTVTAVK-DGKEKTFQVLARLDTEIEADYYRNGGILDYVLRKM 874
****************************9986.7899*****************************97 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (876 nodes)
Target sequences: 1 (881 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 0.03s 00:00:00.05 Elapsed: 00:00:00.04
# Mc/sec: 17.09
//
[ok]
This GapMind analysis is from Apr 09 2024. 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