GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Cup4G11:RR42_RS23515
          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.31967.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: 0.06u 0.03s 00:00:00.09 Elapsed: 00:00:00.08
# Mc/sec: 8.66
//
[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:

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:

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