GapMind for catabolism of small carbon sources

 

Aligments for a candidate for acn in Klebsiella michiganensis M5al

Align Aconitate hydratase B; ACN; Aconitase; (2R,3S)-2-methylisocitrate dehydratase; (2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate dehydratase; 2-methyl-cis-aconitate hydratase; Iron-responsive protein-like; IRP-like; RNA-binding protein; EC 4.2.1.3; EC 4.2.1.99 (characterized)
to candidate BWI76_RS04910 BWI76_RS04910 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase

Query= SwissProt::Q8ZRS8
         (865 letters)



>lcl|FitnessBrowser__Koxy:BWI76_RS04910 BWI76_RS04910 bifunctional
           aconitate hydratase 2/2-methylisocitrate dehydratase
          Length = 872

 Score = 1679 bits (4347), Expect = 0.0
 Identities = 835/865 (96%), Positives = 853/865 (98%)

Query: 1   MLEEYRKHVAERAAQGIVPKPLDATQMAALVELLKTPPVGEEEFLLDLLINRVPPGVDEA 60
           +LEEYRKHVAERAA+GIVPKPLDATQMAALVELLK PP GEEEFLLDLLINRVPPGVDEA
Sbjct: 8   VLEEYRKHVAERAAEGIVPKPLDATQMAALVELLKNPPAGEEEFLLDLLINRVPPGVDEA 67

Query: 61  AYVKAGFLAAVAKGDTTSPLVSPEKAIELLGTMQGGYNIHPLIDALDDAKLAPIAAKALS 120
           AYVKAGFLAA+AKGD TSPLV+ EKA+ELLGTMQGGYNIHPLIDALDDAKLAPIAAKALS
Sbjct: 68  AYVKAGFLAAIAKGDATSPLVTREKAVELLGTMQGGYNIHPLIDALDDAKLAPIAAKALS 127

Query: 121 HTLLMFDNFYDVEEKAKAGNEYAKQVMQSWADAEWFLSRPPLAEKITVTVFKVTGETNTD 180
           HTLLMFDNFYDVEEKAKAGNEYAKQVMQSWADAEWFLSRP LA+KITVTVFKVTGETNTD
Sbjct: 128 HTLLMFDNFYDVEEKAKAGNEYAKQVMQSWADAEWFLSRPQLADKITVTVFKVTGETNTD 187

Query: 181 DLSPAPDAWSRPDIPLHAQAMLKNAREGIEPDQPGVVGPIKQIEALQKKGYPLAYVGDVV 240
           DLSPAPDAWSRPDIPLHA AMLKNAREGI+PDQPG VGPIKQIEALQ+KG+PLAYVGDVV
Sbjct: 188 DLSPAPDAWSRPDIPLHALAMLKNAREGIDPDQPGAVGPIKQIEALQQKGFPLAYVGDVV 247

Query: 241 GTGSSRKSATNSVLWFMGDDIPNVPNKRGGGLCLGGKIAPIFFNTMEDAGALPIEVDVSN 300
           GTGSSRKSATNSVLWFMGDDIPNVPNKRGGGL LGGKIAPIFFNTMEDAGALPIEVDV+N
Sbjct: 248 GTGSSRKSATNSVLWFMGDDIPNVPNKRGGGLVLGGKIAPIFFNTMEDAGALPIEVDVNN 307

Query: 301 LNMGDVIDVYPYKGEVRNHETGELLATFELKTDVLIDEVRAGGRIPLIIGRGLTTKAREA 360
           LNMGDVIDVYP+KGEVRNHETGELLATFELKTDVLIDEVRAGGRIPLIIGRGLTTKAREA
Sbjct: 308 LNMGDVIDVYPFKGEVRNHETGELLATFELKTDVLIDEVRAGGRIPLIIGRGLTTKAREA 367

Query: 361 LGLPHSDVFRQAKDVAESSRGFSLAQKMVGRACGVKGIRPGAYCEPKMTSVGSQDTTGPM 420
           LGLPHS+VFRQAKDVAESSRG+SLAQKMVGRACGV G+RPGAYCEPKMTSVGSQDTTGPM
Sbjct: 368 LGLPHSEVFRQAKDVAESSRGYSLAQKMVGRACGVAGVRPGAYCEPKMTSVGSQDTTGPM 427

Query: 421 TRDELKDLACLGFSADLVMQSFCHTAAYPKPVDVTTHHTLPDFIMNRGGVSLRPGDGVIH 480
           TRDELKDLACLGFS+DLVMQSFCHTAAYPKPVDVTTHHTLPDFIMNRGGVSLRPGDGVIH
Sbjct: 428 TRDELKDLACLGFSSDLVMQSFCHTAAYPKPVDVTTHHTLPDFIMNRGGVSLRPGDGVIH 487

Query: 481 SWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVRFKGKM 540
           SWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVRFKGKM
Sbjct: 488 SWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVRFKGKM 547

Query: 541 QPGITLRDLVHAIPLYAIKQGLLTVEKKGKKNIFSGRILEIEGLPDLKVEQAFELTDASA 600
           QPGITLRDLVHAIPLYAIKQGLLTVEKKGKKNIFSGRILEIEGLPDLKVEQAFELTDASA
Sbjct: 548 QPGITLRDLVHAIPLYAIKQGLLTVEKKGKKNIFSGRILEIEGLPDLKVEQAFELTDASA 607

Query: 601 ERSAAGCTIKLNKEPIVEYLTSNIVLLKWMIAEGYGDRRTLERRIQGMEKWLADPQLLEA 660
           ERSAAGCTIKLNKEPIVEYLTSNIVLLKWMIAEGYGDRRTLERR+QGMEKWLA+P+LLE 
Sbjct: 608 ERSAAGCTIKLNKEPIVEYLTSNIVLLKWMIAEGYGDRRTLERRVQGMEKWLAEPELLEG 667

Query: 661 DADAEYAAVIDIDLADIKEPILCAPNDPDDARLLSDVQGEKIDEVFIGSCMTNIGHFRAA 720
           DADAEYAAVIDIDLADIKEPILCAPNDPDDARLLSDVQGEKIDEVFIGSCMTNIGHFRAA
Sbjct: 668 DADAEYAAVIDIDLADIKEPILCAPNDPDDARLLSDVQGEKIDEVFIGSCMTNIGHFRAA 727

Query: 721 GKLLDNHKGQLPTRLWVAPPTRMDAAQLTEEGYYSVFGKSGARIEIPGCSLCMGNQARVA 780
           GKLLDNHKGQLPTRLWVAPPTRMDAAQLTEEGYYSVFGKSGARIEIPGCSLCMGNQARVA
Sbjct: 728 GKLLDNHKGQLPTRLWVAPPTRMDAAQLTEEGYYSVFGKSGARIEIPGCSLCMGNQARVA 787

Query: 781 DGATVVSTSTRNFPNRLGTGANVFLASAELAAVAALIGKLPTPEEYQTYVAQVDKTAVDT 840
           DGATVVSTSTRNFPNRLGTGANVFLASAELAAVAALIGKLPTPEEYQTYVAQVDKTA DT
Sbjct: 788 DGATVVSTSTRNFPNRLGTGANVFLASAELAAVAALIGKLPTPEEYQTYVAQVDKTAADT 847

Query: 841 YRYLNFDQLSQYTEKADGVIFQTAV 865
           YRYLNFDQL QYTEKADGVIFQTAV
Sbjct: 848 YRYLNFDQLGQYTEKADGVIFQTAV 872


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: 2366
Number of extensions: 73
Number of successful extensions: 1
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: 872
Length adjustment: 42
Effective length of query: 823
Effective length of database: 830
Effective search space:   683090
Effective search space used:   683090
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 BWI76_RS04910 BWI76_RS04910 (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.7743.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 1684.1   0.0          0 1683.8   0.0    1.0  1  lcl|FitnessBrowser__Koxy:BWI76_RS04910  BWI76_RS04910 bifunctional aconi


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Koxy:BWI76_RS04910  BWI76_RS04910 bifunctional aconitate hydratase 2/2-methylisocitrate dehydrata
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1683.8   0.0         0         0       1     844 []       8     861 ..       8     861 .. 1.00

  Alignments for each domain:
  == domain 1  score: 1683.8 bits;  conditional E-value: 0
                               TIGR00117   1 lleeyrkhvaeraaegiaplplnakqvaalvellkndpeaeeefllellidrvppgvdeaayvkagflaai 71 
                                             +leeyrkhvaeraaegi p+pl+a q+aalvellkn+p++eeefll+lli+rvppgvdeaayvkagflaai
  lcl|FitnessBrowser__Koxy:BWI76_RS04910   8 VLEEYRKHVAERAAEGIVPKPLDATQMAALVELLKNPPAGEEEFLLDLLINRVPPGVDEAAYVKAGFLAAI 78 
                                             69********************************************************************* PP

                               TIGR00117  72 akgevksplisaeeavellgtmlggynvepliealeskdkniakaaakalsktllvfdafddveelskt.n 141
                                             akg+++spl++ e+avellgtm+ggyn++pli+al+  d+++a++aakals+tll+fd+f+dvee++k+ n
  lcl|FitnessBrowser__Koxy:BWI76_RS04910  79 AKGDATSPLVTREKAVELLGTMQGGYNIHPLIDALD--DAKLAPIAAKALSHTLLMFDNFYDVEEKAKAgN 147
                                             ************************************..*******************************9* PP

                               TIGR00117 142 eyakqvleswaeaewflnkeelaekitvtvfkvdgetntddlspapdaftrpdiplhalamlknkieeieq 212
                                             eyakqv++swa+aewfl +++la+kitvtvfkv+getntddlspapda++rpdiplhalamlkn++e+i++
  lcl|FitnessBrowser__Koxy:BWI76_RS04910 148 EYAKQVMQSWADAEWFLSRPQLADKITVTVFKVTGETNTDDLSPAPDAWSRPDIPLHALAMLKNAREGIDP 218
                                             *********************************************************************99 PP

                               TIGR00117 213 ..........rikalkqkgvpvayvgdvvgtgssrksatnsvlwflgkdipfvpnkragglvlggkiapif 273
                                                       +i+al+qkg+p+ayvgdvvgtgssrksatnsvlwf+g+dip vpnkr+gglvlggkiapif
  lcl|FitnessBrowser__Koxy:BWI76_RS04910 219 dqpgavgpikQIEALQQKGFPLAYVGDVVGTGSSRKSATNSVLWFMGDDIPNVPNKRGGGLVLGGKIAPIF 289
                                             99********************************************************************* PP

                               TIGR00117 274 fntaedsgalpievdvkdlnegdvikiypykgeitnket.evvatfklkpetlldevraggripliigrgl 343
                                             fnt+ed+galpievdv++ln+gdvi++yp+kge++n+et e++atf+lk+++l+devraggripliigrgl
  lcl|FitnessBrowser__Koxy:BWI76_RS04910 290 FNTMEDAGALPIEVDVNNLNMGDVIDVYPFKGEVRNHETgELLATFELKTDVLIDEVRAGGRIPLIIGRGL 360
                                             **************************************99******************************* PP

                               TIGR00117 344 tdkarealglsesevfkkakapaesakgftlaqklvgkacgvkgirpgtycepkvttvgsqdttgamtrde 414
                                             t+karealgl++sevf++ak++aes++g++laqk+vg+acgv g+rpg+ycepk+t+vgsqdttg+mtrde
  lcl|FitnessBrowser__Koxy:BWI76_RS04910 361 TTKAREALGLPHSEVFRQAKDVAESSRGYSLAQKMVGRACGVAGVRPGAYCEPKMTSVGSQDTTGPMTRDE 431
                                             *********************************************************************** PP

                               TIGR00117 415 lkelaslgfdadlvlqsfchtaaypkpvdvkthktlpdfisqrggvalrpgdgvihswlnrmllpdtvgtg 485
                                             lk+la+lgf++dlv+qsfchtaaypkpvdv th+tlpdfi++rggv+lrpgdgvihswlnrmllpdtvgtg
  lcl|FitnessBrowser__Koxy:BWI76_RS04910 432 LKDLACLGFSSDLVMQSFCHTAAYPKPVDVTTHHTLPDFIMNRGGVSLRPGDGVIHSWLNRMLLPDTVGTG 502
                                             *********************************************************************** PP

                               TIGR00117 486 gdshtrfplgisfpagsglvafaaatgvmpldmpesvlvrfkgelqpgitlrdlvnaipyyaikkglltve 556
                                             gdshtrfp+gisfpagsglvafaaatgvmpldmpesvlvrfkg++qpgitlrdlv+aip+yaik+glltve
  lcl|FitnessBrowser__Koxy:BWI76_RS04910 503 GDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVRFKGKMQPGITLRDLVHAIPLYAIKQGLLTVE 573
                                             *********************************************************************** PP

                               TIGR00117 557 kkgkvnvfngrileieglpdlkveqafeltdasaersaagctiklnkepvieylksnivllkemiaegyed 627
                                             kkgk+n+f+grileieglpdlkveqafeltdasaersaagctiklnkep++eyl snivllk+miaegy+d
  lcl|FitnessBrowser__Koxy:BWI76_RS04910 574 KKGKKNIFSGRILEIEGLPDLKVEQAFELTDASAERSAAGCTIKLNKEPIVEYLTSNIVLLKWMIAEGYGD 644
                                             *********************************************************************** PP

                               TIGR00117 628 krtlkrridamekwlanpelleadadaeyaavieidlaeikepilaapndpddvkllsevagdaidevfig 698
                                             +rtl+rr+++mekwla+pelle+dadaeyaavi+idla+ikepil+apndpdd++lls+v+g++idevfig
  lcl|FitnessBrowser__Koxy:BWI76_RS04910 645 RRTLERRVQGMEKWLAEPELLEGDADAEYAAVIDIDLADIKEPILCAPNDPDDARLLSDVQGEKIDEVFIG 715
                                             *********************************************************************** PP

                               TIGR00117 699 scmtnighfraagkileaak.tvkarlwvvpptrmdeqqlieegyyaifgaagartevpgcslcmgnqarv 768
                                             scmtnighfraagk+l+++k ++++rlwv+pptrmd++ql+eegyy++fg++gar+e+pgcslcmgnqarv
  lcl|FitnessBrowser__Koxy:BWI76_RS04910 716 SCMTNIGHFRAAGKLLDNHKgQLPTRLWVAPPTRMDAAQLTEEGYYSVFGKSGARIEIPGCSLCMGNQARV 786
                                             *******************99************************************************** PP

                               TIGR00117 769 edgatvfststrnfdnrlgkgakvylgsaelaavaallgkiptkeeylalvsekvesakdklyrylnfnel 839
                                             +dgatv+ststrnf+nrlg+ga+v+l+saelaavaal+gk+pt+eey+++v++++++a d +yrylnf++l
  lcl|FitnessBrowser__Koxy:BWI76_RS04910 787 ADGATVVSTSTRNFPNRLGTGANVFLASAELAAVAALIGKLPTPEEYQTYVAQVDKTAAD-TYRYLNFDQL 856
                                             ***********************************************************9.********** PP

                               TIGR00117 840 enfee 844
                                              +++e
  lcl|FitnessBrowser__Koxy:BWI76_RS04910 857 GQYTE 861
                                             **985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (844 nodes)
Target sequences:                          1  (872 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: 8.37
//
[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 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