Aligments for a candidate for acn in Cupriavidus basilensis 4G11

GapMind for catabolism of small carbon sources

Aligments for a candidate for acn in Cupriavidus basilensis 4G11

Align aconitate hydratase (EC 4.2.1.3) (characterized)
to candidate RR42_RS23515 RR42_RS23515 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase

Query= BRENDA::P36683
         (865 letters)



>lcl|FitnessBrowser__Cup4G11:RR42_RS23515 RR42_RS23515 bifunctional
           aconitate hydratase 2/2-methylisocitrate dehydratase
          Length = 861

 Score = 1280 bits (3312), Expect = 0.0
 Identities = 637/862 (73%), Positives = 731/862 (84%), Gaps = 6/862 (0%)

Query: 1   MLEEYRKHVAERAAEGIAPKPLDANQMAALVELLKNPPAGEEEFLLDLLTNRVPPGVDEA 60
           MLE YR HVAERAA GI P PL A Q A L+ELLK+PPAGEE+ L+DL+T+RVP GVD+A
Sbjct: 1   MLENYRAHVAERAALGIPPLPLTAKQTAELIELLKSPPAGEEQVLVDLITHRVPAGVDDA 60

Query: 61  AYVKAGFLAAIAKGEAKSPLLTPEKAIELLGTMQGGYNIHPLIDALDDAKLAPIAAKALS 120
           A VKA +LAA+A G+    L++  KA ELLGTM GGYNI PLI+ LDDA++ P+AA+AL 
Sbjct: 61  AKVKASYLAAVALGKEACALISRAKAAELLGTMLGGYNISPLIELLDDAEIGPVAAEALK 120

Query: 121 HTLLMFDNFYDVEEKAKAGNEYAKQVMQSWADAEWFLNRPALAEKLTVTVFKVTGETNTD 180
            TLLMFD F+DV+EKA  GN  AK V+QSWADAEWF +RP + + LTVTVFKVTGETNTD
Sbjct: 121 KTLLMFDAFHDVKEKADKGNAIAKSVLQSWADAEWFTSRPEVPQSLTVTVFKVTGETNTD 180

Query: 181 DLSPAPDAWSRPDIPLHALAMLKNAREGIEPDQPGVVGPIKQIEALQQKGFPLAYVGDVV 240
           DLSPAPDA +RPDIPLHALAMLKNAR GI P++ G  GP+K IE+L++KG  +AYVGDVV
Sbjct: 181 DLSPAPDATTRPDIPLHALAMLKNARPGITPEEDGKRGPVKFIESLKEKGNLVAYVGDVV 240

Query: 241 GTGSSRKSATNSVLWFMGDDIPHVPNKRGGGLCLGGKIAPIFFNTMEDAGALPIEVDVSN 300
           GTGSSRKSATNSVLWF G+DIP VPNKR GG+CLG KIAPIF+NTMEDAGALPIE+DVS 
Sbjct: 241 GTGSSRKSATNSVLWFTGEDIPFVPNKRFGGVCLGSKIAPIFYNTMEDAGALPIELDVSQ 300

Query: 301 LNMGDVIDVYPYKGEVRNHETGELLATFELKTDVLIDEVRAGGRIPLIIGRGLTTKAREA 360
           + MGDV+++ PY G+   +  G+++A F +K+DVL DEVRAGGRIPLI+GRGLT KAREA
Sbjct: 301 MEMGDVVELRPYDGKALKN--GQVIAEFTVKSDVLFDEVRAGGRIPLIVGRGLTAKAREA 358

Query: 361 LGLPHSDVFRQAKDVAESDRGFSLAQKMVGRACGV---KGIRPGAYCEPKMTSVGSQDTT 417
           LGL  S +FR   + A++ RGF+LAQKMVGRACG+   KGIRPG YCEPKMTSVGSQDTT
Sbjct: 359 LGLAPSTLFRLPHNPADTGRGFTLAQKMVGRACGLPEGKGIRPGTYCEPKMTSVGSQDTT 418

Query: 418 GPMTRDELKDLACLGFSADLVMQSFCHTAAYPKPVDVNTHHTLPDFIMNRGGVSLRPGDG 477
           GPMTRDELKDLACLGFSADLVMQSFCHTAAYPKPVDV THHTLP FI  RGG+SLRPGDG
Sbjct: 419 GPMTRDELKDLACLGFSADLVMQSFCHTAAYPKPVDVKTHHTLPQFISTRGGISLRPGDG 478

Query: 478 VIHSWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVRFK 537
           VIHSWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVRFK
Sbjct: 479 VIHSWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVRFK 538

Query: 538 GKMQPGITLRDLVHAIPLYAIKQGLLTVEKKGKKNIFSGRILEIEGLPDLKVEQAFELTD 597
           GKMQPG+TLRDLV+AIPLYAIK GLLTV K+GKKNIFSGR+LEIEGLPDLKVEQAFEL+D
Sbjct: 539 GKMQPGVTLRDLVNAIPLYAIKSGLLTVAKQGKKNIFSGRVLEIEGLPDLKVEQAFELSD 598

Query: 598 ASAERSAAGCTIKLNKEPIIEYLNSNIVLLKWMIAEGYGDRRTLERRIQGMEKWLANPEL 657
           ASAERSAAGC+++LNKEPIIEY+NSNI LLKWMIAEGY D R+L RRIQ ME WLA+P+L
Sbjct: 599 ASAERSAAGCSVRLNKEPIIEYINSNITLLKWMIAEGYQDPRSLSRRIQAMEAWLADPKL 658

Query: 658 LEADADAEYAAVIDIDLADIKEPILCAPNDPDDARPLSAVQGEKIDEVFIGSCMTNIGHF 717
           LE DADAEYAAVI+IDLAD+ EPI+  PNDPDD + LS V G KIDEVFIGSCMTNIGHF
Sbjct: 659 LEPDADAEYAAVIEIDLADVHEPIVACPNDPDDVKTLSEVAGAKIDEVFIGSCMTNIGHF 718

Query: 718 RAAGKLLDAHKGQLPTRLWVAPPTRMDAAQLTEEGYYSVFGKSGARIEIPGCSLCMGNQA 777
           RAA KLL+  K  +P +LWVAPPT+MDA QLTEEG+Y VFG +GAR E+PGCSLCMGNQA
Sbjct: 719 RAASKLLEG-KRDIPVKLWVAPPTKMDAKQLTEEGHYGVFGTAGARTEMPGCSLCMGNQA 777

Query: 778 RVADGATVVSTSTRNFPNRLGTGANVFLASAELAAVAALIGKLPTPEEYQTYVAQVDKTA 837
           +V +GATV+STSTRNFPNRLG   NV+L SAELAA+ + +G++PT EEY + +  +    
Sbjct: 778 QVREGATVMSTSTRNFPNRLGKNTNVYLGSAELAAICSRLGRIPTKEEYMSDMGVLATNG 837

Query: 838 VDTYRYLNFNQLSQYTEKADGV 859
              Y+YLNF+++  +   AD V
Sbjct: 838 DQIYKYLNFDKIEDFKGVADTV 859


Lambda     K      H
   0.317    0.136    0.400 

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: 2045
Number of extensions: 73
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: 865
Length of database: 861
Length adjustment: 42
Effective length of query: 823
Effective length of database: 819
Effective search space:   674037
Effective search space used:   674037
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 RR42_RS23515 RR42_RS23515 (bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase)
to HMM TIGR00117 (acnB: aconitate hydratase 2 (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/TIGR00117.hmm
# target sequence database:        /tmp/gapView.16278.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00117  [M=844]
Accession:   TIGR00117
Description: acnB: aconitate hydratase 2
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 1518.9   0.0          0 1518.7   0.0    1.0  1  lcl|FitnessBrowser__Cup4G11:RR42_RS23515  RR42_RS23515 bifunctional aconit


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cup4G11:RR42_RS23515  RR42_RS23515 bifunctional aconitate hydratase 2/2-methylisocitrate dehydrat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1518.7   0.0         0         0       1     843 [.       1     853 [.       1     854 [. 0.99

  Alignments for each domain:
  == domain 1  score: 1518.7 bits;  conditional E-value: 0
                                 TIGR00117   1 lleeyrkhvaeraaegiaplplnakqvaalvellkndpeaeeefllellidrvppgvdeaayvkagfla 69 
                                               +le+yr hvaeraa+gi+plpl akq+a+l+ellk +p++ee+ l++l+++rvp gvd+aa+vka +la
  lcl|FitnessBrowser__Cup4G11:RR42_RS23515   1 MLENYRAHVAERAALGIPPLPLTAKQTAELIELLKSPPAGEEQVLVDLITHRVPAGVDDAAKVKASYLA 69 
                                               79******************************************************************* PP

                                 TIGR00117  70 aiakgevksplisaeeavellgtmlggynvepliealeskdkniakaaakalsktllvfdafddveels 138
                                               a+a g+  ++lis  +a ellgtmlggyn+ plie+l+  d++i ++aa+al+ktll+fdaf+dv+e++
  lcl|FitnessBrowser__Cup4G11:RR42_RS23515  70 AVALGKEACALISRAKAAELLGTMLGGYNISPLIELLD--DAEIGPVAAEALKKTLLMFDAFHDVKEKA 136
                                               **************************************..****************************9 PP

                                 TIGR00117 139 kt.neyakqvleswaeaewflnkeelaekitvtvfkvdgetntddlspapdaftrpdiplhalamlknk 206
                                               +  n++ak vl+swa+aewf  ++e+++ +tvtvfkv+getntddlspapda+trpdiplhalamlkn+
  lcl|FitnessBrowser__Cup4G11:RR42_RS23515 137 DKgNAIAKSVLQSWADAEWFTSRPEVPQSLTVTVFKVTGETNTDDLSPAPDATTRPDIPLHALAMLKNA 205
                                               888****************************************************************** PP

                                 TIGR00117 207 ieeieq..........rikalkqkgvpvayvgdvvgtgssrksatnsvlwflgkdipfvpnkragglvl 265
                                               +++i +           i++lk+kg  vayvgdvvgtgssrksatnsvlwf g+dipfvpnkr gg++l
  lcl|FitnessBrowser__Cup4G11:RR42_RS23515 206 RPGITPeedgkrgpvkFIESLKEKGNLVAYVGDVVGTGSSRKSATNSVLWFTGEDIPFVPNKRFGGVCL 274
                                               ****99999*****999**************************************************** PP

                                 TIGR00117 266 ggkiapiffntaedsgalpievdvkdlnegdvikiypykgeitnketevvatfklkpetlldevraggr 334
                                               g kiapif+nt+ed+galpie dv+++++gdv+++ py+g+   k+++v+a f +k+++l+devraggr
  lcl|FitnessBrowser__Cup4G11:RR42_RS23515 275 GSKIAPIFYNTMEDAGALPIELDVSQMEMGDVVELRPYDGKAL-KNGQVIAEFTVKSDVLFDEVRAGGR 342
                                               *****************************************75.566********************** PP

                                 TIGR00117 335 ipliigrgltdkarealglsesevfkkakapaesakgftlaqklvgkacgv...kgirpgtycepkvtt 400
                                               ipli+grglt karealgl++s +f+ +++pa++++gftlaqk+vg+acg+   kgirpgtycepk+t+
  lcl|FitnessBrowser__Cup4G11:RR42_RS23515 343 IPLIVGRGLTAKAREALGLAPSTLFRLPHNPADTGRGFTLAQKMVGRACGLpegKGIRPGTYCEPKMTS 411
                                               **************************************************87779************** PP

                                 TIGR00117 401 vgsqdttgamtrdelkelaslgfdadlvlqsfchtaaypkpvdvkthktlpdfisqrggvalrpgdgvi 469
                                               vgsqdttg+mtrdelk+la+lgf+adlv+qsfchtaaypkpvdvkth+tlp+fis+rgg++lrpgdgvi
  lcl|FitnessBrowser__Cup4G11:RR42_RS23515 412 VGSQDTTGPMTRDELKDLACLGFSADLVMQSFCHTAAYPKPVDVKTHHTLPQFISTRGGISLRPGDGVI 480
                                               ********************************************************************* PP

                                 TIGR00117 470 hswlnrmllpdtvgtggdshtrfplgisfpagsglvafaaatgvmpldmpesvlvrfkgelqpgitlrd 538
                                               hswlnrmllpdtvgtggdshtrfp+gisfpagsglvafaaatgvmpldmpesvlvrfkg++qpg+tlrd
  lcl|FitnessBrowser__Cup4G11:RR42_RS23515 481 HSWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVRFKGKMQPGVTLRD 549
                                               ********************************************************************* PP

                                 TIGR00117 539 lvnaipyyaikkglltvekkgkvnvfngrileieglpdlkveqafeltdasaersaagctiklnkepvi 607
                                               lvnaip+yaik glltv k+gk+n+f+gr+leieglpdlkveqafel+dasaersaagc ++lnkep+i
  lcl|FitnessBrowser__Cup4G11:RR42_RS23515 550 LVNAIPLYAIKSGLLTVAKQGKKNIFSGRVLEIEGLPDLKVEQAFELSDASAERSAAGCSVRLNKEPII 618
                                               ********************************************************************* PP

                                 TIGR00117 608 eylksnivllkemiaegyedkrtlkrridamekwlanpelleadadaeyaavieidlaeikepilaapn 676
                                               ey++sni llk+miaegy+d r+l rri+ame+wla+p+lle+dadaeyaavieidla+++epi+a+pn
  lcl|FitnessBrowser__Cup4G11:RR42_RS23515 619 EYINSNITLLKWMIAEGYQDPRSLSRRIQAMEAWLADPKLLEPDADAEYAAVIEIDLADVHEPIVACPN 687
                                               ********************************************************************* PP

                                 TIGR00117 677 dpddvkllsevagdaidevfigscmtnighfraagkileaaktvkarlwvvpptrmdeqqlieegyyai 745
                                               dpddvk+lsevag +idevfigscmtnighfraa+k+le++++++ +lwv+ppt+md++ql+eeg y++
  lcl|FitnessBrowser__Cup4G11:RR42_RS23515 688 DPDDVKTLSEVAGAKIDEVFIGSCMTNIGHFRAASKLLEGKRDIPVKLWVAPPTKMDAKQLTEEGHYGV 756
                                               ********************************************************************* PP

                                 TIGR00117 746 fgaagartevpgcslcmgnqarvedgatvfststrnfdnrlgkgakvylgsaelaavaallgkiptkee 814
                                               fg+agarte+pgcslcmgnqa+v++gatv+ststrnf+nrlgk ++vylgsaelaa+++ lg+iptkee
  lcl|FitnessBrowser__Cup4G11:RR42_RS23515 757 FGTAGARTEMPGCSLCMGNQAQVREGATVMSTSTRNFPNRLGKNTNVYLGSAELAAICSRLGRIPTKEE 825
                                               ********************************************************************* PP

                                 TIGR00117 815 ylalvsekvesakdklyrylnfnelenfe 843
                                               y++ +  +++++ d++y+ylnf+++e+f+
  lcl|FitnessBrowser__Cup4G11:RR42_RS23515 826 YMSDMG-VLATNGDQIYKYLNFDKIEDFK 853
                                               **9875.889999**************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (844 nodes)
Target sequences:                          1  (861 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 0.01s 00:00:00.06 Elapsed: 00:00:00.07
# Mc/sec: 10.09
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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

GapMind for catabolism of small carbon sources