Alignments for a candidate for acn in Shewanella sp. ANA-3

GapMind for catabolism of small carbon sources

Alignments for a candidate for acn in Shewanella sp. ANA-3

Align aconitate hydratase (EC 4.2.1.3) (characterized)
to candidate 7023199 Shewana3_0433 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase (RefSeq)

Query= BRENDA::P36683
         (865 letters)



>FitnessBrowser__ANA3:7023199
          Length = 890

 Score = 1442 bits (3734), Expect = 0.0
 Identities = 704/865 (81%), Positives = 784/865 (90%)

Query: 1   MLEEYRKHVAERAAEGIAPKPLDANQMAALVELLKNPPAGEEEFLLDLLTNRVPPGVDEA 60
           +LE YRKHVAERAAEG+ PKPLDA+Q+A LV+L++NPPAGEE  +LDLL NR+PPGVDEA
Sbjct: 26  VLEAYRKHVAERAAEGVVPKPLDAHQVAELVKLVQNPPAGEEAVILDLLENRIPPGVDEA 85

Query: 61  AYVKAGFLAAIAKGEAKSPLLTPEKAIELLGTMQGGYNIHPLIDALDDAKLAPIAAKALS 120
           AYVKA FL A+AKG A SP+L+ E+A ELLGTMQGGYNI PLI  LD+  LAP+AAKALS
Sbjct: 86  AYVKAAFLDAVAKGAATSPILSAERATELLGTMQGGYNIEPLIAQLDNPALAPLAAKALS 145

Query: 121 HTLLMFDNFYDVEEKAKAGNEYAKQVMQSWADAEWFLNRPALAEKLTVTVFKVTGETNTD 180
           HTLLMFD+F+DV EK +AGN YAKQV+++WA+A+W+L+RP LA+K+T+TVFKV+GETNTD
Sbjct: 146 HTLLMFDSFHDVVEKMEAGNAYAKQVVEAWANADWYLSRPKLADKVTLTVFKVSGETNTD 205

Query: 181 DLSPAPDAWSRPDIPLHALAMLKNAREGIEPDQPGVVGPIKQIEALQQKGFPLAYVGDVV 240
           DLSPAPDAWSRPDIPLHALAMLKNAR+GIEPD PG VGPIK++E L+ KGFPL YVGDVV
Sbjct: 206 DLSPAPDAWSRPDIPLHALAMLKNARDGIEPDVPGSVGPIKKLEELKTKGFPLVYVGDVV 265

Query: 241 GTGSSRKSATNSVLWFMGDDIPHVPNKRGGGLCLGGKIAPIFFNTMEDAGALPIEVDVSN 300
           GTGSSRKSATNSVLWFMGDDIP VPNKR GG CLGGKIAPIFFNTMEDAGALPIE+DVS 
Sbjct: 266 GTGSSRKSATNSVLWFMGDDIPFVPNKRAGGFCLGGKIAPIFFNTMEDAGALPIELDVSK 325

Query: 301 LNMGDVIDVYPYKGEVRNHETGELLATFELKTDVLIDEVRAGGRIPLIIGRGLTTKAREA 360
           + MGDVID+YPY G+V+ H T E+++ F LKTDVL+DEVRAGGRIPLIIGRGLT KAR  
Sbjct: 326 MEMGDVIDIYPYAGQVKRHGTEEVISEFSLKTDVLLDEVRAGGRIPLIIGRGLTDKARSV 385

Query: 361 LGLPHSDVFRQAKDVAESDRGFSLAQKMVGRACGVKGIRPGAYCEPKMTSVGSQDTTGPM 420
           LGLP SDVF + +D+A+S +G++LAQKMVG+ACGV G+RPG YCEPKMTSVGSQDTTGPM
Sbjct: 386 LGLPASDVFVRPQDIADSGKGYTLAQKMVGKACGVAGVRPGQYCEPKMTSVGSQDTTGPM 445

Query: 421 TRDELKDLACLGFSADLVMQSFCHTAAYPKPVDVNTHHTLPDFIMNRGGVSLRPGDGVIH 480
           TRDELKDLACLGFSADL MQSFCHTAAYPKPVDVNTHHTLPDFIMNRGGVSLRPGDGVIH
Sbjct: 446 TRDELKDLACLGFSADLTMQSFCHTAAYPKPVDVNTHHTLPDFIMNRGGVSLRPGDGVIH 505

Query: 481 SWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVRFKGKM 540
           SWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVRFKGKM
Sbjct: 506 SWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVRFKGKM 565

Query: 541 QPGITLRDLVHAIPLYAIKQGLLTVEKKGKKNIFSGRILEIEGLPDLKVEQAFELTDASA 600
           QPGITLRDLVHAIPL AI+ GLLTVEKKGK NIFSGR+LEIEGL  LKVEQAFEL+DASA
Sbjct: 566 QPGITLRDLVHAIPLKAIEMGLLTVEKKGKINIFSGRVLEIEGLETLKVEQAFELSDASA 625

Query: 601 ERSAAGCTIKLNKEPIIEYLNSNIVLLKWMIAEGYGDRRTLERRIQGMEKWLANPELLEA 660
           ERSAAGCTIKL+KEPIIEYLNSNI +LKWMIAEGYGDRRT+ERRI+GME+WLANPEL+ A
Sbjct: 626 ERSAAGCTIKLDKEPIIEYLNSNITMLKWMIAEGYGDRRTIERRIKGMEEWLANPELMSA 685

Query: 661 DADAEYAAVIDIDLADIKEPILCAPNDPDDARPLSAVQGEKIDEVFIGSCMTNIGHFRAA 720
           D DAEYAAVI+IDL +IKEPILCAPNDPDDA  LS+V   +IDEVF+GSCMTNIGHFRA 
Sbjct: 686 DKDAEYAAVIEIDLNEIKEPILCAPNDPDDAVLLSSVAQTQIDEVFVGSCMTNIGHFRAT 745

Query: 721 GKLLDAHKGQLPTRLWVAPPTRMDAAQLTEEGYYSVFGKSGARIEIPGCSLCMGNQARVA 780
           GK+LD     LPTRLW+APPT+MD  QLTEEGYY +FG+ GARIEIPGCSLCMGNQARVA
Sbjct: 746 GKMLDKFAKTLPTRLWIAPPTKMDKDQLTEEGYYGIFGRVGARIEIPGCSLCMGNQARVA 805

Query: 781 DGATVVSTSTRNFPNRLGTGANVFLASAELAAVAALIGKLPTPEEYQTYVAQVDKTAVDT 840
           +GATVVSTSTRNFPNRLGTGANV+LASAELAAVAAL+G+LPT EEYQ Y  ++D TA DT
Sbjct: 806 EGATVVSTSTRNFPNRLGTGANVYLASAELAAVAALLGRLPTVEEYQEYAKELDATAADT 865

Query: 841 YRYLNFNQLSQYTEKADGVIFQTAV 865
           YRYLNF+Q+  YT+KA  VIFQ+AV
Sbjct: 866 YRYLNFDQIDSYTKKASQVIFQSAV 890


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: 2153
Number of extensions: 74
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: 890
Length adjustment: 43
Effective length of query: 822
Effective length of database: 847
Effective search space:   696234
Effective search space used:   696234
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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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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 paper from 2022 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