Alignments for a candidate for acn in Pseudomonas benzenivorans DSM 8628

GapMind for catabolism of small carbon sources

Alignments for a candidate for acn in Pseudomonas benzenivorans DSM 8628

Align aconitate hydratase (EC 4.2.1.3) (characterized)
to candidate WP_090438471.1 BLS63_RS00850 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase

Query= BRENDA::P36683
         (865 letters)



>NCBI__GCF_900100495.1:WP_090438471.1
          Length = 869

 Score = 1373 bits (3554), Expect = 0.0
 Identities = 674/859 (78%), Positives = 755/859 (87%), Gaps = 3/859 (0%)

Query: 1   MLEEYRKHVAERAAEGIAPKPLDANQMAALVELLKNPPAGEEEFLLDLLTNRVPPGVDEA 60
           MLE YRKHVAERAA+GI P+PL+A Q A LVELLKNPPAGEE FL+DL+TNRVP GVDEA
Sbjct: 1   MLEAYRKHVAERAAQGIVPQPLNAEQTAGLVELLKNPPAGEEAFLVDLITNRVPAGVDEA 60

Query: 61  AYVKAGFLAAIAKGEAKSPLLTPEKAIELLGTMQGGYNIHPLIDALDDAKLAPIAAKALS 120
           AYVKAGFL+A+AKGE  SPLL+  +A+ELLGTMQGGYNI  L++ LD+A+LA +AA+ L 
Sbjct: 61  AYVKAGFLSALAKGEVSSPLLSKTRAVELLGTMQGGYNITTLVELLDNAELAAVAAEQLK 120

Query: 121 HTLLMFDNFYDVEEKAKAGNEYAKQVMQSWADAEWFLNRPALAEKLTVTVFKVTGETNTD 180
           HTLLMFD F+DV EKAKAGN  AK V+ SWA+ EWF NR A+ EK+T+TVFKVTGETNTD
Sbjct: 121 HTLLMFDAFHDVAEKAKAGNANAKAVLASWAEGEWFQNRAAVPEKVTLTVFKVTGETNTD 180

Query: 181 DLSPAPDAWSRPDIPLHALAMLKNAREGIEPDQPGVVGPIKQIEALQQKGFPLAYVGDVV 240
           DLSPAPDAWSRPDIPLHALAMLK AR+GIEPDQPG VGPIKQ+EAL+ KGFP+AYVGDVV
Sbjct: 181 DLSPAPDAWSRPDIPLHALAMLKMARDGIEPDQPGSVGPIKQMEALKAKGFPVAYVGDVV 240

Query: 241 GTGSSRKSATNSVLWFMGDDIPHVPNKRGGGLCLGGKIAPIFFNTMEDAGALPIEVDVSN 300
           GTGSSRKSATNSVLWF GDDIP+VPNKR GG C G KIAPIF+NTMEDAGALPIE D +N
Sbjct: 241 GTGSSRKSATNSVLWFFGDDIPNVPNKRAGGFCFGTKIAPIFYNTMEDAGALPIEFDCTN 300

Query: 301 LNMGDVIDVYPYKGEVRNHETGELLATFELKTDVLIDEVRAGGRIPLIIGRGLTTKAREA 360
           L MGDVIDVYP KGEVR H + EL+ +F+LKTDVL+DEVRAGGRIPLI+GRGLT KAR  
Sbjct: 301 LAMGDVIDVYPIKGEVRRHGSDELVTSFQLKTDVLLDEVRAGGRIPLIVGRGLTEKARAE 360

Query: 361 LGLPHSDVFRQAKDVAESDRGFSLAQKMVGRACGV---KGIRPGAYCEPKMTSVGSQDTT 417
           LGL  S +F + +  A+S +GF+LAQKMVGRACG+   +G+RPG YCEPKMT+VGSQDTT
Sbjct: 361 LGLAPSTLFNKPESPADSGKGFTLAQKMVGRACGLAEGQGVRPGTYCEPKMTTVGSQDTT 420

Query: 418 GPMTRDELKDLACLGFSADLVMQSFCHTAAYPKPVDVNTHHTLPDFIMNRGGVSLRPGDG 477
           GPMTRDELKDLACLGFSADLVMQSFCHTAAYPKP+DV THHTLPDFI  RGGVSLRPGDG
Sbjct: 421 GPMTRDELKDLACLGFSADLVMQSFCHTAAYPKPIDVTTHHTLPDFIRTRGGVSLRPGDG 480

Query: 478 VIHSWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVRFK 537
           +IHSWLNRMLLPDTVGTGGDSHTRFP+GISFPAGSGLVAFAAATGVMPLDMPESVLVRFK
Sbjct: 481 IIHSWLNRMLLPDTVGTGGDSHTRFPMGISFPAGSGLVAFAAATGVMPLDMPESVLVRFK 540

Query: 538 GKMQPGITLRDLVHAIPLYAIKQGLLTVEKKGKKNIFSGRILEIEGLPDLKVEQAFELTD 597
           GK+QPGITLRDLVHAIP YAIK GLLTVEKKGK N FSGRILEIEGL +L VEQAFEL+D
Sbjct: 541 GKLQPGITLRDLVHAIPYYAIKAGLLTVEKKGKINAFSGRILEIEGLDELTVEQAFELSD 600

Query: 598 ASAERSAAGCTIKLNKEPIIEYLNSNIVLLKWMIAEGYGDRRTLERRIQGMEKWLANPEL 657
           ASAERSAAGCTIKL ++ I EYL SNI LL+WMI EGYGD RTLERR + ME WLANP+L
Sbjct: 601 ASAERSAAGCTIKLPEKAIAEYLQSNITLLRWMIGEGYGDARTLERRAKAMEAWLANPQL 660

Query: 658 LEADADAEYAAVIDIDLADIKEPILCAPNDPDDARPLSAVQGEKIDEVFIGSCMTNIGHF 717
           LEAD DAEYA +I+IDLA+I EP+LCAPNDPDDAR LS+V GEKIDEVFIGSCMTNIGHF
Sbjct: 661 LEADKDAEYAEIIEIDLAEINEPVLCAPNDPDDARLLSSVAGEKIDEVFIGSCMTNIGHF 720

Query: 718 RAAGKLLDAHKGQLPTRLWVAPPTRMDAAQLTEEGYYSVFGKSGARIEIPGCSLCMGNQA 777
           RAAGKLLD  KG +PTRLW+APPT+MDA QLTEEGYY ++GK+GAR+E+PGCSLCMGNQA
Sbjct: 721 RAAGKLLDKVKGGIPTRLWLAPPTKMDAHQLTEEGYYGIYGKAGARMEMPGCSLCMGNQA 780

Query: 778 RVADGATVVSTSTRNFPNRLGTGANVFLASAELAAVAALIGKLPTPEEYQTYVAQVDKTA 837
           RV  G+TVVSTSTRNFPNRLG   NV+LASAELAAVA++IGKLP+ EEY  Y   +D  A
Sbjct: 781 RVQTGSTVVSTSTRNFPNRLGDATNVYLASAELAAVASIIGKLPSVEEYMQYAKDIDSMA 840

Query: 838 VDTYRYLNFNQLSQYTEKA 856
            D YRYL+F+Q++++ E A
Sbjct: 841 ADVYRYLSFDQIAEFREAA 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: 2177
Number of extensions: 78
Number of successful extensions: 2
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: 869
Length adjustment: 42
Effective length of query: 823
Effective length of database: 827
Effective search space:   680621
Effective search space used:   680621
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 24 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
the source code
instructions for running GapMind on your computer

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