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_090447774.1 BLS63_RS21135 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase

Query= BRENDA::P36683
         (865 letters)



>NCBI__GCF_900100495.1:WP_090447774.1
          Length = 866

 Score = 1369 bits (3544), Expect = 0.0
 Identities = 667/856 (77%), Positives = 753/856 (87%)

Query: 1   MLEEYRKHVAERAAEGIAPKPLDANQMAALVELLKNPPAGEEEFLLDLLTNRVPPGVDEA 60
           MLE YR HVA RA +G+ P  L+A Q A LVELLKNPPAGEEE LLDL+TNRVPPGVDEA
Sbjct: 1   MLEAYRNHVAARAEQGLPPLALNAEQTAGLVELLKNPPAGEEEVLLDLITNRVPPGVDEA 60

Query: 61  AYVKAGFLAAIAKGEAKSPLLTPEKAIELLGTMQGGYNIHPLIDALDDAKLAPIAAKALS 120
           AYVKAGFL+A+AKG A SPLL+  +A+ELLGTMQGGYNI  L++ LDDA+L  +AA+ L 
Sbjct: 61  AYVKAGFLSAVAKGAAGSPLLSKTRAVELLGTMQGGYNIATLVELLDDAELGSVAAEQLK 120

Query: 121 HTLLMFDNFYDVEEKAKAGNEYAKQVMQSWADAEWFLNRPALAEKLTVTVFKVTGETNTD 180
           HTLLMFD F+DV EKAKAGN +AK V+QSWAD EWF  RPA+AEK +++VFKVTGETNTD
Sbjct: 121 HTLLMFDAFHDVAEKAKAGNAHAKAVLQSWADGEWFTKRPAIAEKYSLSVFKVTGETNTD 180

Query: 181 DLSPAPDAWSRPDIPLHALAMLKNAREGIEPDQPGVVGPIKQIEALQQKGFPLAYVGDVV 240
           DLSPAPDAWSRPDIPLHALAMLK AR+GIEP+Q G +GP+KQI A++ KGFP+AYVGDVV
Sbjct: 181 DLSPAPDAWSRPDIPLHALAMLKMARDGIEPEQQGAIGPLKQIAAIKAKGFPVAYVGDVV 240

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

Query: 301 LNMGDVIDVYPYKGEVRNHETGELLATFELKTDVLIDEVRAGGRIPLIIGRGLTTKAREA 360
           L MGDVIDVYPY G+V  H + +++  FELKT+VL+DEVRAGGRIPLI+GRGLT KAR  
Sbjct: 301 LEMGDVIDVYPYAGKVCKHGSDQVITRFELKTEVLLDEVRAGGRIPLIVGRGLTEKARAE 360

Query: 361 LGLPHSDVFRQAKDVAESDRGFSLAQKMVGRACGVKGIRPGAYCEPKMTSVGSQDTTGPM 420
           LGL  S++F +    A+S +GF+LAQKMVG+ACGV G+RPG YCEPKMT+VGSQDTTGPM
Sbjct: 361 LGLGVSELFNKPVAPADSGKGFTLAQKMVGKACGVTGVRPGTYCEPKMTTVGSQDTTGPM 420

Query: 421 TRDELKDLACLGFSADLVMQSFCHTAAYPKPVDVNTHHTLPDFIMNRGGVSLRPGDGVIH 480
           TRDELKDLACLGFSADLVMQSFCHTAAYPKPVDVNTHHTLPDF+ +RGGVSL+PGDG+IH
Sbjct: 421 TRDELKDLACLGFSADLVMQSFCHTAAYPKPVDVNTHHTLPDFMRSRGGVSLKPGDGIIH 480

Query: 481 SWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVRFKGKM 540
           SWLNRMLLPDTVGTGGDSHTRFP+GISFPAGSGLVAFAAATGVMPLDMPESVLVRFKGK+
Sbjct: 481 SWLNRMLLPDTVGTGGDSHTRFPMGISFPAGSGLVAFAAATGVMPLDMPESVLVRFKGKL 540

Query: 541 QPGITLRDLVHAIPLYAIKQGLLTVEKKGKKNIFSGRILEIEGLPDLKVEQAFELTDASA 600
           QPGITLRDLVHAIP YAI++GLLTVEKKGK N FSGRILEIEGL +L VEQAFEL+DASA
Sbjct: 541 QPGITLRDLVHAIPYYAIQKGLLTVEKKGKINAFSGRILEIEGLDELTVEQAFELSDASA 600

Query: 601 ERSAAGCTIKLNKEPIIEYLNSNIVLLKWMIAEGYGDRRTLERRIQGMEKWLANPELLEA 660
           ERSAAGCTIKL ++ I EYL SNI LL+WMI EGYGD RTLERR Q ME WLANP+L+ A
Sbjct: 601 ERSAAGCTIKLPEKAIAEYLQSNITLLRWMIGEGYGDARTLERRAQAMEAWLANPQLMSA 660

Query: 661 DADAEYAAVIDIDLADIKEPILCAPNDPDDARPLSAVQGEKIDEVFIGSCMTNIGHFRAA 720
           DADAEYA V++IDLA+I +PILCAPNDPDDAR LS+VQGEKIDEVFIGSCMTNIGHFRAA
Sbjct: 661 DADAEYAEVVEIDLAEINQPILCAPNDPDDARLLSSVQGEKIDEVFIGSCMTNIGHFRAA 720

Query: 721 GKLLDAHKGQLPTRLWVAPPTRMDAAQLTEEGYYSVFGKSGARIEIPGCSLCMGNQARVA 780
           GKLLD  KG +PTRLW++PPT+MDA QLTEEGYY ++GK+GAR+E+PGCSLCMGNQARVA
Sbjct: 721 GKLLDKVKGGIPTRLWLSPPTKMDAHQLTEEGYYGIYGKAGARMEMPGCSLCMGNQARVA 780

Query: 781 DGATVVSTSTRNFPNRLGTGANVFLASAELAAVAALIGKLPTPEEYQTYVAQVDKTAVDT 840
             ATVVSTSTRNFPNRLG GANV+LASAELAAVAA+ GKLPT EEY  Y   +D  A D 
Sbjct: 781 ANATVVSTSTRNFPNRLGDGANVYLASAELAAVAAITGKLPTVEEYMAYAKDIDSMAADV 840

Query: 841 YRYLNFNQLSQYTEKA 856
           YRYL+F+Q++++ E A
Sbjct: 841 YRYLSFDQIAEFREAA 856


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: 2127
Number of extensions: 76
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: 866
Length adjustment: 42
Effective length of query: 823
Effective length of database: 824
Effective search space:   678152
Effective search space used:   678152
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