Alignments for a candidate for acn in Pseudomonas stutzeri RCH2

GapMind for catabolism of small carbon sources

Alignments for a candidate for acn in Pseudomonas stutzeri RCH2

Align aconitate hydratase (EC 4.2.1.3) (characterized)
to candidate GFF2264 Psest_2309 aconitate hydratase 2

Query= BRENDA::P36683
         (865 letters)



>FitnessBrowser__psRCH2:GFF2264
          Length = 875

 Score = 1387 bits (3591), Expect = 0.0
 Identities = 678/860 (78%), Positives = 762/860 (88%), Gaps = 3/860 (0%)

Query: 1   MLEEYRKHVAERAAEGIAPKPLDANQMAALVELLKNPPAGEEEFLLDLLTNRVPPGVDEA 60
           +LE YRKHV ERAA+G+ P+PL+A Q A LVELLKNPPAGEEEFL+DL+TNRVP GVDEA
Sbjct: 7   VLEAYRKHVEERAAQGVVPQPLNAEQTAGLVELLKNPPAGEEEFLVDLITNRVPAGVDEA 66

Query: 61  AYVKAGFLAAIAKGEAKSPLLTPEKAIELLGTMQGGYNIHPLIDALDDAKLAPIAAKALS 120
           AYVKAGFL+A+AKGE  SPLL+ ++A+ELLGTMQGGYNI  L++ LD A+L  +AA+ L 
Sbjct: 67  AYVKAGFLSALAKGETSSPLLSKQRAVELLGTMQGGYNISTLVELLDSAELGAVAAEQLK 126

Query: 121 HTLLMFDNFYDVEEKAKAGNEYAKQVMQSWADAEWFLNRPALAEKLTVTVFKVTGETNTD 180
           HTLLMFD F+DV EKAKAGNE+AK VMQSWA+ EWF NRPA+AEK++++VFKVTGETNTD
Sbjct: 127 HTLLMFDAFHDVAEKAKAGNEHAKAVMQSWAEGEWFTNRPAVAEKVSLSVFKVTGETNTD 186

Query: 181 DLSPAPDAWSRPDIPLHALAMLKNAREGIEPDQPGVVGPIKQIEALQQKGFPLAYVGDVV 240
           DLSPAPDAWSRPDIPLHALAMLK AR+GI PD PG VGPIKQ+E L+ KGFP+AYVGDVV
Sbjct: 187 DLSPAPDAWSRPDIPLHALAMLKMARDGINPDVPGSVGPIKQMEELKAKGFPVAYVGDVV 246

Query: 241 GTGSSRKSATNSVLWFMGDDIPHVPNKRGGGLCLGGKIAPIFFNTMEDAGALPIEVDVSN 300
           GTGSSRKSATNSVLWF GDDIP+VPNKR GG C G KIAPIF+NTMEDAGALPIE D SN
Sbjct: 247 GTGSSRKSATNSVLWFFGDDIPNVPNKRAGGFCFGTKIAPIFYNTMEDAGALPIEFDCSN 306

Query: 301 LNMGDVIDVYPYKGEVRNHETGELLATFELKTDVLIDEVRAGGRIPLIIGRGLTTKAREA 360
           L MGDVIDVYPY G+V  H T E++ TFELKTDVL+DEVRAGGRIPLIIGRGLT KAR  
Sbjct: 307 LAMGDVIDVYPYAGKVCKHGTDEVITTFELKTDVLLDEVRAGGRIPLIIGRGLTEKARAE 366

Query: 361 LGLPHSDVFRQAKDVAESDRGFSLAQKMVGRACGV---KGIRPGAYCEPKMTSVGSQDTT 417
           +GL  S +F++ +  A+S +GF+LAQKMVGRACG+   KG+RPG YCEPKMT+VGSQDTT
Sbjct: 367 MGLAPSTLFKKPEAPADSGKGFTLAQKMVGRACGLPEGKGVRPGTYCEPKMTTVGSQDTT 426

Query: 418 GPMTRDELKDLACLGFSADLVMQSFCHTAAYPKPVDVNTHHTLPDFIMNRGGVSLRPGDG 477
           GPMTRDELKDLACLGFSADLVMQSFCHTAAYPKP+DVNTHHTLPDFIMNR GVSLRPGDG
Sbjct: 427 GPMTRDELKDLACLGFSADLVMQSFCHTAAYPKPIDVNTHHTLPDFIMNRSGVSLRPGDG 486

Query: 478 VIHSWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVRFK 537
           +IHSWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVRFK
Sbjct: 487 IIHSWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVRFK 546

Query: 538 GKMQPGITLRDLVHAIPLYAIKQGLLTVEKKGKKNIFSGRILEIEGLPDLKVEQAFELTD 597
           G+MQPGITLRDLVHAIP YAI+QGLLTVEKKGKKNIFSGRILEIEGL  L VEQAFEL+D
Sbjct: 547 GQMQPGITLRDLVHAIPYYAIQQGLLTVEKKGKKNIFSGRILEIEGLNQLTVEQAFELSD 606

Query: 598 ASAERSAAGCTIKLNKEPIIEYLNSNIVLLKWMIAEGYGDRRTLERRIQGMEKWLANPEL 657
           ASAERSAAGCTIKL ++ I EYL SNI +L+WMI+EGYGD RTLERR Q ME WLA+P+L
Sbjct: 607 ASAERSAAGCTIKLPEDSIAEYLKSNITMLRWMISEGYGDARTLERRAQAMEAWLADPKL 666

Query: 658 LEADADAEYAAVIDIDLADIKEPILCAPNDPDDARPLSAVQGEKIDEVFIGSCMTNIGHF 717
           LEAD DAEYAAVI+IDLA++KEP+LCAPNDPDDAR LS V GEKIDEVFIGSCMTNIGHF
Sbjct: 667 LEADKDAEYAAVIEIDLAEVKEPVLCAPNDPDDARLLSTVAGEKIDEVFIGSCMTNIGHF 726

Query: 718 RAAGKLLDAHKGQLPTRLWVAPPTRMDAAQLTEEGYYSVFGKSGARIEIPGCSLCMGNQA 777
           RAAGKLLD  KG +PTRLW+APPT+MDA QLTEEGYY ++GK+GAR+E+PGCSLCMGNQA
Sbjct: 727 RAAGKLLDKVKGGIPTRLWLAPPTKMDAHQLTEEGYYGIYGKAGARMEMPGCSLCMGNQA 786

Query: 778 RVADGATVVSTSTRNFPNRLGTGANVFLASAELAAVAALIGKLPTPEEYQTYVAQVDKTA 837
           RV  G+TVVSTSTRNFPNRLG   NV+LASAELAAVA++IGKLPT  EY  Y   +D  A
Sbjct: 787 RVQTGSTVVSTSTRNFPNRLGDATNVYLASAELAAVASIIGKLPTVAEYMEYAKNIDSMA 846

Query: 838 VDTYRYLNFNQLSQYTEKAD 857
            D YRYL+F+Q++++ + A+
Sbjct: 847 ADIYRYLSFDQIAEFRDAAE 866


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: 2188
Number of extensions: 70
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: 875
Length adjustment: 42
Effective length of query: 823
Effective length of database: 833
Effective search space:   685559
Effective search space used:   685559
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
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