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_022948414.1 H035_RS0107715 aconitate hydratase AcnA
Query= SwissProt::Q5SMF6
(902 letters)
>NCBI__GCF_000421465.1:WP_022948414.1
Length = 901
Score = 1078 bits (2789), Expect = 0.0
Identities = 540/894 (60%), Positives = 672/894 (75%), Gaps = 9/894 (1%)
Query: 5 FQTLKTLTTKSGTYGYYDLQELERKGVAEVSRLPFSIRVMLESLLRNEDGYQVTREDIEA 64
F + L T +G GY++L LE + + EV+ LPF+I+V+LES+LR+ DG + +D+ A
Sbjct: 7 FGSRAELNTAAGKLGYFNLARLEAENLGEVTALPFTIKVLLESILRHCDGKLIREQDVAA 66
Query: 65 LARWRPD-PGEINVPLKLARVILQDFTGVPAVVDLAAMRDAIKAKGGDPKRINPVVPADL 123
LA W P VP ARV+LQDFTGVPA+VDLAAMR A++ G P ++ P++PADL
Sbjct: 67 LAGWNPTGDNRAEVPFMPARVLLQDFTGVPALVDLAAMRQAVQRLGKQPAQVEPLIPADL 126
Query: 124 VIDHSVQVDAFGTAYAFFYNVEKEYERNRERYLLLKWAQNALENFRVVPPGTGIVHQVNI 183
V+DHS+QVDAFG+ A N+ E+ERN ERY LKW Q A E+F+VVPPG GIVHQVN+
Sbjct: 127 VVDHSIQVDAFGSPEALKQNMALEFERNLERYQFLKWGQQAFESFKVVPPGVGIVHQVNL 186
Query: 184 EYLTKVVMTGKRDGLTLAFPDSLVGTDSHTTMVNGLGVLGWGVGGIEAEAVMLGQPYYML 243
EYL + V +DG+ +PDSLVGTDSHTTM+NGLG+LGWGVGGIEAEA MLGQP YML
Sbjct: 187 EYLARGVFC--QDGIV--YPDSLVGTDSHTTMINGLGILGWGVGGIEAEAGMLGQPLYML 242
Query: 244 APRVVGFKLYGELPEGATATDLVLTVTEMLRKHGVVGKFVEFYGPGVAKLSTPDRATIAN 303
P V+GF+L G LPEGATATDLVL +TEMLR HGVVGKFVEF+GPG++ +S PDRAT+AN
Sbjct: 243 PPEVIGFELTGALPEGATATDLVLRITEMLRAHGVVGKFVEFFGPGLSTISVPDRATVAN 302
Query: 304 MAPEYGATMGFFPVDEETLNYLRQTGRPEELVELVEAYTKAVGLFRTPEAEEKVQYSEYL 363
MAPEYGAT+GFFPVD L Y+R TGRP++ VEL+E Y KA GLFRT + ++SE L
Sbjct: 303 MAPEYGATVGFFPVDAAVLEYMRATGRPQDRVELIETYYKAQGLFRTDDTPAP-RFSEVL 361
Query: 364 ELDLSAVEPSLAGPKRPQDRVPLKEVKKSFLAHLTKPVKERGFGLSEDQLQRKVLVKRRD 423
LDLS VEPSLAGP+RPQDRV + ++ +F LT+P E GFG+ + V V
Sbjct: 362 RLDLSTVEPSLAGPRRPQDRVAVGALRDAFRQALTRPASEAGFGVPPAEKDAAVSVSVDG 421
Query: 424 EEFELTHGSVVIAAITSCTNTSNPSVMLGAGLLAKKAVEAGLDRKPWVKTSLAPGSKVVT 483
+ EL HGSVVIAAITSCTNTSNPSVML AGL+AKKA E GL VKTSLAPGS+VVT
Sbjct: 422 RKAELKHGSVVIAAITSCTNTSNPSVMLSAGLVAKKAAEKGLKPSVSVKTSLAPGSRVVT 481
Query: 484 DYLEMSGLMPFLEALGFHLVGYGCTTCIGNSGPLPEDIAKAVEEGNLVVAAVLSGNRNFE 543
DYL+ SGL+P+LEA+GF+ VGYGCTTCIGNSGPLPE +AK ++ G LV AAVLSGNRNFE
Sbjct: 482 DYLQESGLLPYLEAIGFYTVGYGCTTCIGNSGPLPEAVAKGIQSGRLVAAAVLSGNRNFE 541
Query: 544 GRINPHVKANYLASPMLVVAYALAGRMDIDFTTEPLGFDPNGKPIYLKDIWPSMEEIREA 603
GR++P +ANYLASP LVVAYALAG +DID T EPLG D G+P+YL+DIWP+ EE+
Sbjct: 542 GRVHPLTRANYLASPPLVVAYALAGTVDIDLTREPLGTDKEGRPVYLRDIWPTREELEAV 601
Query: 604 IRKTLDPELFKKEYSKVFEGDERWQALPAPTGELYQWDPESTYIQNPPFFEDLGER--KV 661
++ DPE F + Y+ + + + W A+ P LY W PESTYIQ PPFF+ + + +
Sbjct: 602 LKTASDPEKFNRVYTHLDDFNPEWNAIQVPASVLYDWPPESTYIQEPPFFQKMQPQPEPI 661
Query: 662 EDIRGARVLLVLGDSVTTDHISPAGAIPVKSPAGQYLISKGVKPEDFNSYGSRRGNHEVM 721
+ I GARVL ++GDSVTTDHISPAG IP + PA +YL SKGV +DFN++G+RRGNHEVM
Sbjct: 662 QPIEGARVLAMMGDSVTTDHISPAGVIP-EGPAAEYLRSKGVGEKDFNTFGARRGNHEVM 720
Query: 722 MRGTFANIRIKNLMLDGIEGGYAKKLPEGDVDFVYNVAMRYKAEGTPLLVIAGKEYGTGS 781
MRGTFANIR+KNL++ G EGG P G+ ++++ AMRY+AE PL+V+AGK+YG GS
Sbjct: 721 MRGTFANIRLKNLLVPGKEGGVTIHFPGGEETWIFDAAMRYQAEEVPLIVLAGKDYGMGS 780
Query: 782 SRDWAAKGTYLLGIRAVLAESFERIHRSNLVGMGVLPLEFLPGENRETLGLTGYEVYDIL 841
SRDWAAKG LLG++AV+AESFERIHRSNLVGMG+LPL F PG++ +LGLTG E Y I
Sbjct: 781 SRDWAAKGPRLLGVKAVIAESFERIHRSNLVGMGILPLTFKPGDSARSLGLTGRERYRIP 840
Query: 842 GLEDLKPRKLVDIVARREDGSEVRFQAIARLDTPVEVDYYKNGGILQTVLLNML 895
E L + + A +DG+++ F A RL++ E++YY+NGGILQTVL NML
Sbjct: 841 ADETLAVGAELTVTAEADDGTKISFPADVRLNSAAELEYYRNGGILQTVLRNML 894
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: 2266
Number of extensions: 108
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: 901
Length adjustment: 43
Effective length of query: 859
Effective length of database: 858
Effective search space: 737022
Effective search space used: 737022
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_022948414.1 H035_RS0107715 (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.1165163.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 1337.4 0.0 0 1337.2 0.0 1.0 1 NCBI__GCF_000421465.1:WP_022948414.1
Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000421465.1:WP_022948414.1
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1337.2 0.0 0 0 4 876 .] 21 894 .. 18 894 .. 0.98
Alignments for each domain:
== domain 1 score: 1337.2 bits; conditional E-value: 0
TIGR01341 4 yyyslkalees.lekisklpkslrillesvlrnldgskikeedveallkwkkeelkdeeiafkparvvlqdft 75
y++l +le + l++++ lp ++++lles+lr++dg+ i+e+dv al+ w+ + + e++f+parv+lqdft
NCBI__GCF_000421465.1:WP_022948414.1 21 GYFNLARLEAEnLGEVTALPFTIKVLLESILRHCDGKLIREQDVAALAGWNPTGDNRAEVPFMPARVLLQDFT 93
59999999865499*********************************************************** PP
TIGR01341 76 Gvpavvdlaalreavknlgkdpekinplvpvdlvidhsvqvdkageeealeanvelefernkerykflkwakk 148
Gvpa+vdlaa+r+av++lgk p++++pl+p+dlv+dhs+qvd +g+ eal++n+ lefern ery+flkw+++
NCBI__GCF_000421465.1:WP_022948414.1 94 GVPALVDLAAMRQAVQRLGKQPAQVEPLIPADLVVDHSIQVDAFGSPEALKQNMALEFERNLERYQFLKWGQQ 166
************************************************************************* PP
TIGR01341 149 afknlkvvppgtGivhqvnleylakvvfeaekdgellaypdslvGtdshttminGlGvlGwGvGGieaeaall 221
af+ +kvvppg Givhqvnleyla+ vf ++ ++ypdslvGtdshttminGlG+lGwGvGGieaea++l
NCBI__GCF_000421465.1:WP_022948414.1 167 AFESFKVVPPGVGIVHQVNLEYLARGVFCQD----GIVYPDSLVGTDSHTTMINGLGILGWGVGGIEAEAGML 235
****************************987....79************************************ PP
TIGR01341 222 GqpvslsvpeviGvkltGklreGvtatdlvltvtellrkkgvvgkfveffGeglkelsladratianmapeyG 294
Gqp+++ peviG+ ltG l eG tatdlvl++te+lr +gvvgkfveffG+gl+++s++drat+anmapeyG
NCBI__GCF_000421465.1:WP_022948414.1 236 GQPLYMLPPEVIGFELTGALPEGATATDLVLRITEMLRAHGVVGKFVEFFGPGLSTISVPDRATVANMAPEYG 308
************************************************************************* PP
TIGR01341 295 ataaffpiddvtlqylrltgrdedkvelvekylkaqelfvd.dseepkytdvveldlsdveasvaGpkrpqdr 366
at++ffp+d+ l+y+r tgr++d+vel+e y kaq+lf++ d+ p++++v+ ldls+ve+s+aGp+rpqdr
NCBI__GCF_000421465.1:WP_022948414.1 309 ATVGFFPVDAAVLEYMRATGRPQDRVELIETYYKAQGLFRTdDTPAPRFSEVLRLDLSTVEPSLAGPRRPQDR 381
***************************************9956777*************************** PP
TIGR01341 367 valkevkaafksslesnagekglalr....keakekklegkeaelkdgavviaaitsctntsnpsvllgagll 435
va+ ++++af+++l ++a+e g++++ a++ ++g++aelk+g+vviaaitsctntsnpsv+l+agl+
NCBI__GCF_000421465.1:WP_022948414.1 382 VAVGALRDAFRQALTRPASEAGFGVPpaekDAAVSVSVDGRKAELKHGSVVIAAITSCTNTSNPSVMLSAGLV 454
*************************95553345566778********************************** PP
TIGR01341 436 akkavelGlkvkpyvktslapGskvvtdylaesgllpyleelGfnlvGyGcttciGnsGpleeeveeaikend 508
akka e Glk vktslapGs+vvtdyl+esgllpyle++Gf+ vGyGcttciGnsGpl+e+v++ i+ +
NCBI__GCF_000421465.1:WP_022948414.1 455 AKKAAEKGLKPSVSVKTSLAPGSRVVTDYLQESGLLPYLEAIGFYTVGYGCTTCIGNSGPLPEAVAKGIQSGR 527
************************************************************************* PP
TIGR01341 509 levsavlsGnrnfegrihplvkanylaspplvvayalaGtvdidlekepigtdkdGkkvylkdiwpsakeiae 581
l+++avlsGnrnfegr+hpl++anylaspplvvayalaGtvdidl++ep+gtdk+G++vyl+diwp+ +e+++
NCBI__GCF_000421465.1:WP_022948414.1 528 LVAAAVLSGNRNFEGRVHPLTRANYLASPPLVVAYALAGTVDIDLTREPLGTDKEGRPVYLRDIWPTREELEA 600
************************************************************************* PP
TIGR01341 582 lvkkavkkelfkkeyeevtegnerwnelevtssdlyewdekstyireppffeelklepeevedikgarillll 654
+ k+a +e f++ y ++ + n +wn ++v+ s ly+w ++styi+eppff++++ +pe +++i+gar+l+++
NCBI__GCF_000421465.1:WP_022948414.1 601 VLKTASDPEKFNRVYTHLDDFNPEWNAIQVPASVLYDWPPESTYIQEPPFFQKMQPQPEPIQPIEGARVLAMM 673
************************************************************************* PP
TIGR01341 655 GdsittdhispaGsikkdspaakylkekGverrdfnsyGsrrGnhevmlrGtfaniriknklvkgkeGgltvy 727
Gds+ttdhispaG i ++ paa+yl+ kGv ++dfn++G+rrGnhevm+rGtfanir+kn lv+gkeGg+t++
NCBI__GCF_000421465.1:WP_022948414.1 674 GDSVTTDHISPAGVI-PEGPAAEYLRSKGVGEKDFNTFGARRGNHEVMMRGTFANIRLKNLLVPGKEGGVTIH 745
*************88.789****************************************************** PP
TIGR01341 728 lpdsevvsvydaamkykkegvplvvlaGkeyGsGssrdwaakgtkllGvkaviaesferihrsnlvgmGvlpl 800
+p +e++ ++daam+y+ e+vpl+vlaGk+yG+Gssrdwaakg++llGvkaviaesferihrsnlvgmG+lpl
NCBI__GCF_000421465.1:WP_022948414.1 746 FPGGEETWIFDAAMRYQAEEVPLIVLAGKDYGMGSSRDWAAKGPRLLGVKAVIAESFERIHRSNLVGMGILPL 818
************************************************************************* PP
TIGR01341 801 efkqgedaetlgltgeetidvddieelkpkkevtvelvkedgeketveavlridtevelayvkkgGilqyvlr 873
+fk g++a +lgltg+e+ ++ e+l ++e+tv++ +dg k+++ a +r+++++el+y+++gGilq vlr
NCBI__GCF_000421465.1:WP_022948414.1 819 TFKPGDSARSLGLTGRERYRIPADETLAVGAELTVTAEADDGTKISFPADVRLNSAAELEYYRNGGILQTVLR 891
*****************9999999************************************************* PP
TIGR01341 874 kll 876
++l
NCBI__GCF_000421465.1:WP_022948414.1 892 NML 894
*97 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (876 nodes)
Target sequences: 1 (901 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 43.51
//
[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