GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Koxy:BWI76_RS04910
          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)

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