Align Aconitate hydratase A; 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_012969327.1 ALVIN_RS00390 Fe/S-dependent 2-methylisocitrate dehydratase AcnD
Query= SwissProt::Q937N8
(869 letters)
>NCBI__GCF_000025485.1:WP_012969327.1
Length = 863
Score = 1491 bits (3860), Expect = 0.0
Identities = 745/868 (85%), Positives = 798/868 (91%), Gaps = 7/868 (0%)
Query: 1 MNSANRKPLPGTKLDYFDARAAVEAIQPGAYDKLPYTSRVLAENLVRRCDPATLTDSLLQ 60
MN+ NRKPLPGT LDYFDARAA+EAI PGAYD+LPYT+RVLAENLVRRCDPA L+DSL Q
Sbjct: 1 MNTTNRKPLPGTDLDYFDARAAIEAIAPGAYDRLPYTARVLAENLVRRCDPAILSDSLRQ 60
Query: 61 LVGRKRDLDFPWFPARVVCHDILGQTALVDLAGLRDAIADQGGDPAKVNPVVPVQLIVDH 120
+V KR+ DFPWFPARVVCHDILGQTALVDLAGLRDAIADQGGDPAKVNPVVPVQL+VDH
Sbjct: 61 IVECKRERDFPWFPARVVCHDILGQTALVDLAGLRDAIADQGGDPAKVNPVVPVQLVVDH 120
Query: 121 SLAVECGGFDPDAFAKNRAIEDRRNEDRFHFIDWTKQAFKNVDVIPPGNGIMHQINLEKM 180
SLAVECGG+DPDAFAKNRAIEDRRNEDRFHFI+WTK AF NVDVIP GNGIMHQINLE+M
Sbjct: 121 SLAVECGGYDPDAFAKNRAIEDRRNEDRFHFIEWTKLAFDNVDVIPAGNGIMHQINLERM 180
Query: 181 SPVIHADNGVAYPDTCVGTDSHTPHVDALGVIAIGVGGLEAENVMLGRASWMRLPDIVGV 240
SPVI A +GVA+PDT VGTDSHTPHVDALGVIA+GVGGLEAENVMLGRASWMRLP+I+GV
Sbjct: 181 SPVIQARDGVAFPDTLVGTDSHTPHVDALGVIAVGVGGLEAENVMLGRASWMRLPEIIGV 240
Query: 241 ELTGKRQPGITATDIVLALTEFLRKEKVVGAYLEFRGEGASSLTLGDRATISNMAPEYGA 300
ELTGK QPGITATD+VLALTEFLRKEKVVGAYLEF GEGA++LT+GDRA+ISNM PEYGA
Sbjct: 241 ELTGKPQPGITATDVVLALTEFLRKEKVVGAYLEFHGEGAAALTIGDRASISNMCPEYGA 300
Query: 301 TAAMFFIDEQTIDYLRLTGRTDEQLKLVETYARTAGLWADSLKNAEYERVLKFDLSSVVR 360
TAA+F ID QTIDYLRLTGR D Q+KLVETYA+ GLWA++LKNA+YER LKFDLSSVVR
Sbjct: 301 TAALFHIDAQTIDYLRLTGRDDAQVKLVETYAKQTGLWAETLKNAQYERTLKFDLSSVVR 360
Query: 361 NMAGPSNPHKRLPTSALAERGIAVDLDKASAQEAEGLMPDGAVIIAAITSCTNTSNPRNV 420
N+AGPSNPH R+ T+ LA +GIA D E G MPDGAVIIAAITSCTNTSNPRNV
Sbjct: 361 NLAGPSNPHARVATADLAAKGIAGQWD-----EVPGQMPDGAVIIAAITSCTNTSNPRNV 415
Query: 421 IAAALLARNANARGLARKPWVKSSLAPGSKAVELYLEEANLLPDLEKLGFGIVAFACTTC 480
IAA LLARNAN GL RKPWVKSSLAPGSK V LYLEEA LL +LE+LGFGIV FACTTC
Sbjct: 416 IAAGLLARNANRLGLTRKPWVKSSLAPGSKTVPLYLEEAGLLLELEQLGFGIVGFACTTC 475
Query: 481 NGMSGALDPKIQQEIIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTI 540
NGMSGALDPKIQQEIIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTI
Sbjct: 476 NGMSGALDPKIQQEIIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTI 535
Query: 541 RFDIEKDVLGTDQDGKPVYLKDIWPSDEEIDAIVAKSVKPEQFRKVYEPMFAITAASGES 600
RFDIEKDVL DG+ + LKDIWPSDEEIDA+VA SVKPEQFR+VYEPMFA+ A +GE
Sbjct: 536 RFDIEKDVLAV-ADGREIRLKDIWPSDEEIDAVVAASVKPEQFRQVYEPMFAVRAETGEK 594
Query: 601 VSPLYDWRPQSTYIRRPPYWEGALAGERTLKALRPLAVLGDNITTDHLSPSNAIMLNSAA 660
VSPLYDWRPQSTYIRRPPYWEGALAGERTLK +RPLAVL DNITTDHLSPSNAI+ NSAA
Sbjct: 595 VSPLYDWRPQSTYIRRPPYWEGALAGERTLKGMRPLAVLPDNITTDHLSPSNAILPNSAA 654
Query: 661 GEYLARMGLPEEDFNSYATHRGDHLTAQRATFANPTLINEMAVVDGQVKKGSLARIEPEG 720
GEYLARMGLPEEDFNSYATHRGDHLTAQRATFANP LINEMAVVDGQVK+GSLAR+EP+G
Sbjct: 655 GEYLARMGLPEEDFNSYATHRGDHLTAQRATFANPKLINEMAVVDGQVKQGSLARVEPDG 714
Query: 721 KVVRMWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEVIVAEGFERIHRTN 780
V+RMWEAIETYM+R QPLI+IAGADYGQGSSRDWAAKGVRLAGVEVIVAEGFERIHRTN
Sbjct: 715 TVMRMWEAIETYMNRNQPLIVIAGADYGQGSSRDWAAKGVRLAGVEVIVAEGFERIHRTN 774
Query: 781 LIGMGVLPLEFKPGVNRLTLGLDGTETYDVIGERQPRATLTLVVNRKNGERVEVPVTCRL 840
LIGMGVLPLEFKPGVNR TLG+DGTETYDVIGER+PRA LTLV+ RKNGERVEVPVTCRL
Sbjct: 775 LIGMGVLPLEFKPGVNRKTLGIDGTETYDVIGERRPRADLTLVIQRKNGERVEVPVTCRL 834
Query: 841 DSDEEVSIYEAGGVL-HFAQDFLESSRA 867
D+ EEVSIYEAGGVL FAQDFLES++A
Sbjct: 835 DTAEEVSIYEAGGVLQRFAQDFLESTKA 862
Lambda K H
0.318 0.135 0.398
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: 2258
Number of extensions: 82
Number of successful extensions: 4
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: 869
Length of database: 863
Length adjustment: 42
Effective length of query: 827
Effective length of database: 821
Effective search space: 678967
Effective search space used: 678967
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 WP_012969327.1 ALVIN_RS00390 (Fe/S-dependent 2-methylisocitrate dehydratase AcnD)
to HMM TIGR02333 (acnD: 2-methylisocitrate dehydratase, Fe/S-dependent (EC 4.2.1.99))
# 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/TIGR02333.hmm
# target sequence database: /tmp/gapView.688552.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: TIGR02333 [M=858]
Accession: TIGR02333
Description: 2met_isocit_dHY: 2-methylisocitrate dehydratase, Fe/S-dependent
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 1814.0 0.1 0 1813.9 0.1 1.0 1 NCBI__GCF_000025485.1:WP_012969327.1
Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000025485.1:WP_012969327.1
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1813.9 0.1 0 0 1 858 [] 2 858 .. 2 858 .. 1.00
Alignments for each domain:
== domain 1 score: 1813.9 bits; conditional E-value: 0
TIGR02333 1 ntkyrkalpgtdldyfdaraaveaikpgaydklpytsrvlaenlvrrvdpetleaslkqlierkreldfpwyp 73
nt+ rk+lpgtdldyfdaraa+eai+pgayd+lpyt+rvlaenlvrr+dp+ l++sl+q++e kre dfpw+p
NCBI__GCF_000025485.1:WP_012969327.1 2 NTTNRKPLPGTDLDYFDARAAIEAIAPGAYDRLPYTARVLAENLVRRCDPAILSDSLRQIVECKRERDFPWFP 74
7899********************************************************************* PP
TIGR02333 74 arvvchdilgqtalvdlaglrdaiaekggdpaqvnpvvetqlivdhslaveyggfdpdafeknraiedrrned 146
arvvchdilgqtalvdlaglrdaia++ggdpa+vnpvv++ql+vdhslave+gg+dpdaf+knraiedrrned
NCBI__GCF_000025485.1:WP_012969327.1 75 ARVVCHDILGQTALVDLAGLRDAIADQGGDPAKVNPVVPVQLVVDHSLAVECGGYDPDAFAKNRAIEDRRNED 147
************************************************************************* PP
TIGR02333 147 rfhfinwtkkafknvdvipagngimhqinlekmspvvqvkegvafpdtlvgtdshtphvdalgviaigvggle 219
rfhfi+wtk af+nvdvipagngimhqinle+mspv+q+++gvafpdtlvgtdshtphvdalgvia+gvggle
NCBI__GCF_000025485.1:WP_012969327.1 148 RFHFIEWTKLAFDNVDVIPAGNGIMHQINLERMSPVIQARDGVAFPDTLVGTDSHTPHVDALGVIAVGVGGLE 220
************************************************************************* PP
TIGR02333 220 aetvmlgraslmrlpdivgveltgkrqpgitatdivlalteflrkekvvsayleffgegakaltlgdratisn 292
ae+vmlgras+mrlp+i+gveltgk qpgitatd+vlalteflrkekvv+aylef+gega alt+gdra+isn
NCBI__GCF_000025485.1:WP_012969327.1 221 AENVMLGRASWMRLPEIIGVELTGKPQPGITATDVVLALTEFLRKEKVVGAYLEFHGEGAAALTIGDRASISN 293
************************************************************************* PP
TIGR02333 293 mtpeygataamfaideqtidylkltgreeeqvklvetyakaaglwadslkkavyervlkfdlssvvrnlagps 365
m+peygataa+f id qtidyl+ltgr+++qvklvetyak +glwa++lk+a+yer+lkfdlssvvrnlagps
NCBI__GCF_000025485.1:WP_012969327.1 294 MCPEYGATAALFHIDAQTIDYLRLTGRDDAQVKLVETYAKQTGLWAETLKNAQYERTLKFDLSSVVRNLAGPS 366
************************************************************************* PP
TIGR02333 366 npharlatsdlaakgiakeveeeaeglmpdgaviiaaitsctntsnprnvvaagllarnanklglkrkpwvks 438
nphar+at+dlaakgia++++e++ g+mpdgaviiaaitsctntsnprnv+aagllarnan+lgl+rkpwvks
NCBI__GCF_000025485.1:WP_012969327.1 367 NPHARVATADLAAKGIAGQWDEVP-GQMPDGAVIIAAITSCTNTSNPRNVIAAGLLARNANRLGLTRKPWVKS 438
************************.************************************************ PP
TIGR02333 439 slapgskvvklyleeagllkeleklgfgivafacttcngmsgaldpviqqeiidrdlyatavlsgnrnfdgri 511
slapgsk+v lyleeagll ele+lgfgiv+facttcngmsgaldp+iqqeiidrdlyatavlsgnrnfdgri
NCBI__GCF_000025485.1:WP_012969327.1 439 SLAPGSKTVPLYLEEAGLLLELEQLGFGIVGFACTTCNGMSGALDPKIQQEIIDRDLYATAVLSGNRNFDGRI 511
************************************************************************* PP
TIGR02333 512 hpyakqaflaspplvvayaiagtirfdiekdvlgvdadgkeirlkdiwpsdeeidavvaaavkpeqfrkvyip 584
hpyakqaflaspplvvayaiagtirfdiekdvl v adg+eirlkdiwpsdeeidavvaa+vkpeqfr+vy+p
NCBI__GCF_000025485.1:WP_012969327.1 512 HPYAKQAFLASPPLVVAYAIAGTIRFDIEKDVLAV-ADGREIRLKDIWPSDEEIDAVVAASVKPEQFRQVYEP 583
***********************************.************************************* PP
TIGR02333 585 mfdle.daqkkvsplydwrpmstyirrppywegalagertlkgmrplavlgdnittdhlspsnailldsaage 656
mf++ ++++kvsplydwrp+styirrppywegalagertlkgmrplavl+dnittdhlspsnail +saage
NCBI__GCF_000025485.1:WP_012969327.1 584 MFAVRaETGEKVSPLYDWRPQSTYIRRPPYWEGALAGERTLKGMRPLAVLPDNITTDHLSPSNAILPNSAAGE 656
****999****************************************************************** PP
TIGR02333 657 ylakmglpeedfnsyathrgdhltaqratfanpklfnemvkedgkvkqgslariepegkvtrmweaietymnr 729
yla+mglpeedfnsyathrgdhltaqratfanpkl+nem+ +dg+vkqgslar+ep+g+v+rmweaietymnr
NCBI__GCF_000025485.1:WP_012969327.1 657 YLARMGLPEEDFNSYATHRGDHLTAQRATFANPKLINEMAVVDGQVKQGSLARVEPDGTVMRMWEAIETYMNR 729
************************************************************************* PP
TIGR02333 730 kqpliiiagadygqgssrdwaakgvrlagveaivaegferihrtnlvgmgvlplefkpgtnrktlaldgtevy 802
+qpli+iagadygqgssrdwaakgvrlagve ivaegferihrtnl+gmgvlplefkpg+nrktl++dgte+y
NCBI__GCF_000025485.1:WP_012969327.1 730 NQPLIVIAGADYGQGSSRDWAAKGVRLAGVEVIVAEGFERIHRTNLIGMGVLPLEFKPGVNRKTLGIDGTETY 802
************************************************************************* PP
TIGR02333 803 dvvgeitpradltlvvtrkngeklevpvtcrldtaeevsvyeaggvlqrfaqdfle 858
dv+ge++pradltlv++rknge++evpvtcrldtaeevs+yeaggvlqrfaqdfle
NCBI__GCF_000025485.1:WP_012969327.1 803 DVIGERRPRADLTLVIQRKNGERVEVPVTCRLDTAEEVSIYEAGGVLQRFAQDFLE 858
******************************************************97 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (858 nodes)
Target sequences: 1 (863 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: 00:00:00.03
# Mc/sec: 24.56
//
[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