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_090439551.1 BLS63_RS00675 Fe/S-dependent 2-methylisocitrate dehydratase AcnD
Query= SwissProt::Q937N8
(869 letters)
>NCBI__GCF_900100495.1:WP_090439551.1
Length = 869
Score = 1422 bits (3682), Expect = 0.0
Identities = 710/870 (81%), Positives = 779/870 (89%), Gaps = 4/870 (0%)
Query: 1 MNSANRKPLPGTKLDYFDARAAVEAIQPGAYDKLPYTSRVLAENLVRRCDPATLTDSLLQ 60
MNS RKPL GT LDYFD R AV+AI PGAY KLPYTSRVLAE LVRRC+P LTDSL Q
Sbjct: 1 MNSQYRKPLAGTVLDYFDTREAVDAIAPGAYAKLPYTSRVLAEQLVRRCEPDALTDSLKQ 60
Query: 61 LVGRKRDLDFPWFPARVVCHDILGQTALVDLAGLRDAIADQGGDPAKVNPVVPVQLIVDH 120
L+ RKRDLDFPW+PARVVCHDILGQTALVDLAGLRDAIA++GGDP+KVNPVVP QLIVDH
Sbjct: 61 LIERKRDLDFPWYPARVVCHDILGQTALVDLAGLRDAIAEKGGDPSKVNPVVPTQLIVDH 120
Query: 121 SLAVECGGFDPDAFAKNRAIEDRRNEDRFHFIDWTKQAFKNVDVIPPGNGIMHQINLEKM 180
SLAVE GFDPDAFAKNRAIEDRRNEDRFHFI+WTK AFKNVDVIP GNGIMHQINLEKM
Sbjct: 121 SLAVEAPGFDPDAFAKNRAIEDRRNEDRFHFIEWTKTAFKNVDVIPAGNGIMHQINLEKM 180
Query: 181 SPVIHADNGVAYPDTCVGTDSHTPHVDALGVIAIGVGGLEAENVMLGRASWMRLPDIVGV 240
SPVI A GVA+PDTCVGTDSHTPHVDALGVIAIGVGGLEAE VMLG S MRLPDIVGV
Sbjct: 181 SPVIQARGGVAFPDTCVGTDSHTPHVDALGVIAIGVGGLEAETVMLGLPSMMRLPDIVGV 240
Query: 241 ELTGKRQPGITATDIVLALTEFLRKEKVVGAYLEFRGEGASSLTLGDRATISNMAPEYGA 300
+LTGKRQPGITATDIVLA+TEFLRKE+VVGAY+EF GEGA SL++GDRATISNM PEYGA
Sbjct: 241 KLTGKRQPGITATDIVLAITEFLRKERVVGAYVEFFGEGADSLSIGDRATISNMCPEYGA 300
Query: 301 TAAMFFIDEQTIDYLRLTGRTDEQLKLVETYARTAGLWADSLKNAEYERVLKFDLSSVVR 360
TA+MF+ID+QTIDYL+LTGR EQ+ LVE YA+ GLWAD+L AEYERVL+FDLS+VVR
Sbjct: 301 TASMFYIDQQTIDYLKLTGREPEQVALVENYAKLTGLWADALVTAEYERVLEFDLSTVVR 360
Query: 361 NMAGPSNPHKRLPTSALAERGIAVDLDKAS--AQEAEGLMPDGAVIIAAITSCTNTSNPR 418
NMAGPSNPHKRLPTSAL ERGIA + AS +EAEGL+PDGAVIIAAITSCTNTSNPR
Sbjct: 361 NMAGPSNPHKRLPTSALHERGIADEAKLASGKVEEAEGLLPDGAVIIAAITSCTNTSNPR 420
Query: 419 NVIAAALLARNANARGLARKPWVKSSLAPGSKAVELYLEEANLLPDLEKLGFGIVAFACT 478
NV+AA LLA+ ANA GL RKPWVK+S APGSK +LYLE+A LL +LE+LGFGIV +ACT
Sbjct: 421 NVVAAGLLAKKANALGLLRKPWVKTSFAPGSKVAKLYLEDAGLLSELEQLGFGIVGYACT 480
Query: 479 TCNGMSGALDPKIQQEIIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAG 538
TCNGMSGALDP IQQEIIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAG
Sbjct: 481 TCNGMSGALDPVIQQEIIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAG 540
Query: 539 TIRFDIEKDVLGTDQDGKPVYLKDIWPSDEEIDAIVAKSVKPEQFRKVYEPMFAITAASG 598
T+RFDIE+DVLGTD++G + LKD+WPSDEEIDAIVA SVKPEQF+++Y PMF +
Sbjct: 541 TVRFDIEQDVLGTDKNGNLITLKDLWPSDEEIDAIVAASVKPEQFKQIYIPMFDLGTIQ- 599
Query: 599 ESVSPLYDWRPQSTYIRRPPYWEGALAGERTLKALRPLAVLGDNITTDHLSPSNAIMLNS 658
E+ SPLYDWRP STYIRRPPYWEGALAGERTLK +RPLA+L DNITTDHLSPSNAI+L+S
Sbjct: 600 EAESPLYDWRPMSTYIRRPPYWEGALAGERTLKGMRPLAILPDNITTDHLSPSNAILLDS 659
Query: 659 AAGEYLARMGLPEEDFNSYATHRGDHLTAQRATFANPTLINEMAVVDGQVKKGSLARIEP 718
AAGEYL +MGLPEEDFNSYATHRGDHLTAQRATFANP L+NEMAVVDG VKKGSLAR+EP
Sbjct: 660 AAGEYLHKMGLPEEDFNSYATHRGDHLTAQRATFANPQLVNEMAVVDGVVKKGSLARVEP 719
Query: 719 EGKVVRMWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEVIVAEGFERIHR 778
EGKV+RMWEAIETYM+RKQ LII+AGADYGQGSSRDWAAKGVRLAGVEVIVAEGFERIHR
Sbjct: 720 EGKVMRMWEAIETYMNRKQNLIIVAGADYGQGSSRDWAAKGVRLAGVEVIVAEGFERIHR 779
Query: 779 TNLIGMGVLPLEFKPGVNRLTLGLDGTETYDVIGERQPRATLTLVVNRKNGERVEVPVTC 838
TNL+GMGVLP+EFKPG RLTLGLDG+ETYD+ G+ PR L LV++R+NGE +VPVTC
Sbjct: 780 TNLVGMGVLPVEFKPGTTRLTLGLDGSETYDIEGDVSPRCELILVIHRRNGEVTQVPVTC 839
Query: 839 RLDSDEEVSIYEAGGVL-HFAQDFLESSRA 867
RLD+ EV +Y+AGGVL FAQDFLE + A
Sbjct: 840 RLDTAAEVHVYKAGGVLQRFAQDFLEGAIA 869
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: 2209
Number of extensions: 78
Number of successful extensions: 3
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: 869
Length adjustment: 42
Effective length of query: 827
Effective length of database: 827
Effective search space: 683929
Effective search space used: 683929
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_090439551.1 BLS63_RS00675 (Fe/S-dependent 2-methylisocitrate dehydratase AcnD)
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.27677.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
------- ------ ----- ------- ------ ----- ---- -- -------- -----------
2.2e-289 947.9 0.0 2.7e-289 947.6 0.0 1.0 1 lcl|NCBI__GCF_900100495.1:WP_090439551.1 BLS63_RS00675 Fe/S-dependent 2-m
Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_900100495.1:WP_090439551.1 BLS63_RS00675 Fe/S-dependent 2-methylisocitrate dehydratase AcnD
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 947.6 0.0 2.7e-289 2.7e-289 16 874 .. 29 862 .. 13 864 .. 0.95
Alignments for each domain:
== domain 1 score: 947.6 bits; conditional E-value: 2.7e-289
TIGR01341 16 ekisklpkslrillesvlrnldgskikeedveallkwkkeelkdeeiafkparvvlqdftGvpavvdla 84
+ klp++ r+l e+++r+++ ++++ +++l+ e ++d + ++ parvv d G a+vdla
lcl|NCBI__GCF_900100495.1:WP_090439551.1 29 GAYAKLPYTSRVLAEQLVRRCEPDALTDS-LKQLI----ERKRDLDFPWYPARVVCHDILGQTALVDLA 92
45689*****************9999875.55555....55678************************* PP
TIGR01341 85 alreavknlgkdpekinplvpvdlvidhsvqvdkag.eeealeanvelefernkerykflkwakkafkn 152
lr+a+++ g+dp+k+np+vp l++dhs+ v+ g + +a+++n +e rn++r++f++w+k afkn
lcl|NCBI__GCF_900100495.1:WP_090439551.1 93 GLRDAIAEKGGDPSKVNPVVPTQLIVDHSLAVEAPGfDPDAFAKNRAIEDRRNEDRFHFIEWTKTAFKN 161
**********************************994569***************************** PP
TIGR01341 153 lkvvppgtGivhqvnleylakvvfeaekdgellaypdslvGtdshttminGlGvlGwGvGGieaeaall 221
+ v+p g+Gi+hq+nle ++ v+ + +a+pd+ vGtdsht ++ lGv+ GvGG+eae+++l
lcl|NCBI__GCF_900100495.1:WP_090439551.1 162 VDVIPAGNGIMHQINLEKMSPVIQARG----GVAFPDTCVGTDSHTPHVDALGVIAIGVGGLEAETVML 226
*********************998776....79************************************ PP
TIGR01341 222 GqpvslsvpeviGvkltGklreGvtatdlvltvtellrkkgvvgkfveffGeglkelsladratianma 290
G p+++ +p+++GvkltGk ++G+tatd+vl +te+lrk+ vvg +veffGeg ++ls+ drati+nm+
lcl|NCBI__GCF_900100495.1:WP_090439551.1 227 GLPSMMRLPDIVGVKLTGKRQPGITATDIVLAITEFLRKERVVGAYVEFFGEGADSLSIGDRATISNMC 295
********************************************************************* PP
TIGR01341 291 peyGataaffpiddvtlqylrltgrdedkvelvekylkaqelfvddseepkytdvveldlsdveasvaG 359
peyGata++f id++t++yl+ltgr+ ++v lve+y+k+ +l+ d ++y +v+e dls+v ++aG
lcl|NCBI__GCF_900100495.1:WP_090439551.1 296 PEYGATASMFYIDQQTIDYLKLTGREPEQVALVENYAKLTGLWADALVTAEYERVLEFDLSTVVRNMAG 364
*********************************************99********************** PP
TIGR01341 360 pkrpqdrvalkevkaafksslesnagekglalrkeakekklegkeaelkdgavviaaitsctntsnpsv 428
p +p++r++ +++++ +g+a + + + k+e+ e l dgav+iaaitsctntsnp
lcl|NCBI__GCF_900100495.1:WP_090439551.1 365 PSNPHKRLPTSALHE------------RGIADEAKLASGKVEEAEGLLPDGAVIIAAITSCTNTSNPRN 421
*********999888............3444444555666799999*********************** PP
TIGR01341 429 llgagllakkavelGlkvkpyvktslapGskvvtdylaesgllpyleelGfnlvGyGcttciGnsGple 497
+++agllakka lGl +kp+vkts apGskv yl ++gll+ le+lGf +vGy cttc G sG l+
lcl|NCBI__GCF_900100495.1:WP_090439551.1 422 VVAAGLLAKKANALGLLRKPWVKTSFAPGSKVAKLYLEDAGLLSELEQLGFGIVGYACTTCNGMSGALD 490
********************************************************************* PP
TIGR01341 498 eeveeaikendlevsavlsGnrnfegrihplvkanylaspplvvayalaGtvdidlekepigtdkdGkk 566
++++i + dl ++avlsGnrnf+grihp k ++laspplvvaya+aGtv d+e++ +gtdk+G+
lcl|NCBI__GCF_900100495.1:WP_090439551.1 491 PVIQQEIIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTVRFDIEQDVLGTDKNGNL 559
********************************************************************* PP
TIGR01341 567 vylkdiwpsakeiaelvkkavkkelfkkeyeevtegnerwnelevtssdlyewdekstyireppffeel 635
+ lkd+wps +ei+++v +vk+e fk+ y +++ +++ ++s+ly+w + styir+pp++e+
lcl|NCBI__GCF_900100495.1:WP_090439551.1 560 ITLKDLWPSDEEIDAIVAASVKPEQFKQIYIPMFD----LGTIQEAESPLYDWRPMSTYIRRPPYWEGA 624
**********************************7....789*************************98 PP
TIGR01341 636 klepeevedikgarillllGdsittdhispaGsikkdspaakylkekGverrdfnsyGsrrGnhevmlr 704
+ +kg+r l+ l d+ittdh+sp+ +i ds a++yl++ G+ ++dfnsy + rG+h r
lcl|NCBI__GCF_900100495.1:WP_090439551.1 625 LA---GERTLKGMRPLAILPDNITTDHLSPSNAILLDSAAGEYLHKMGLPEEDFNSYATHRGDHLTAQR 690
87...56789*********************************************************** PP
TIGR01341 705 Gtfaniriknkl..vkg..keGgltvylpdsevvsvydaamkykkegvplvvlaGkeyGsGssrdwaak 769
tfan +++n++ v+g k+G+l++ p+++v+ +++a y + +++l+++aG++yG+Gssrdwaak
lcl|NCBI__GCF_900100495.1:WP_090439551.1 691 ATFANPQLVNEMavVDGvvKKGSLARVEPEGKVMRMWEAIETYMNRKQNLIIVAGADYGQGSSRDWAAK 759
**********984355644689*********************************************** PP
TIGR01341 770 gtkllGvkaviaesferihrsnlvgmGvlplefkqgedaetlgltgeetidvddieelkpkkevtvelv 838
g +l Gv +++ae ferihr+nlvgmGvlp+efk g+++ tlgl+g+et d++ +++p+ e+ +++
lcl|NCBI__GCF_900100495.1:WP_090439551.1 760 GVRLAGVEVIVAEGFERIHRTNLVGMGVLPVEFKPGTTRLTLGLDGSETYDIE--GDVSPRCELILVIH 826
*****************************************************..9************* PP
TIGR01341 839 kedgeketveavlridtevelayvkkgGilqyvlrk 874
+++ge++ v +++r+dt++e++ +k gG+lq ++
lcl|NCBI__GCF_900100495.1:WP_090439551.1 827 RRNGEVTQVPVTCRLDTAAEVHVYKAGGVLQRFAQD 862
******************************977665 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (876 nodes)
Target sequences: 1 (869 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: 0.05u 0.02s 00:00:00.07 Elapsed: 00:00:00.06
# Mc/sec: 11.64
//
[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