Alignments for a candidate for acn in Pseudomonas taeanensis MS-3

GapMind for catabolism of small carbon sources

Alignments for a candidate for acn in Pseudomonas taeanensis MS-3

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 WP_025165718.1 TMS3_RS13040 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase

Query= SwissProt::Q8ZRS8
         (865 letters)



>NCBI__GCF_000498575.2:WP_025165718.1
          Length = 869

 Score = 1359 bits (3517), Expect = 0.0
 Identities = 659/859 (76%), Positives = 753/859 (87%), Gaps = 3/859 (0%)

Query: 1   MLEEYRKHVAERAAQGIVPKPLDATQMAALVELLKTPPVGEEEFLLDLLINRVPPGVDEA 60
           MLE YRKHVAERAAQGIVP+PL+A Q A L+ELLK PP GE+ FLLDL+ NRVPPGVDEA
Sbjct: 1   MLEAYRKHVAERAAQGIVPQPLNAEQTAGLIELLKNPPAGEQAFLLDLITNRVPPGVDEA 60

Query: 61  AYVKAGFLAAVAKGDTTSPLVSPEKAIELLGTMQGGYNIHPLIDALDDAKLAPIAAKALS 120
           AYVKAGFL+A+AKG+ TSPL+S + A+ELLGTMQGGYNI  +++ LDD++LA + A+ L 
Sbjct: 61  AYVKAGFLSAIAKGEATSPLISKQHAVELLGTMQGGYNIATMVELLDDSELAGVTAEQLK 120

Query: 121 HTLLMFDNFYDVEEKAKAGNEYAKQVMQSWADAEWFLSRPPLAEKITVTVFKVTGETNTD 180
           HTLLMFD F+DV EKAK GN +A+ V+QSWAD EWF +RP LA+KI++ VFKVTGETNTD
Sbjct: 121 HTLLMFDAFHDVAEKAKNGNAHAQGVLQSWADGEWFKNRPTLADKISLRVFKVTGETNTD 180

Query: 181 DLSPAPDAWSRPDIPLHAQAMLKNAREGIEPDQPGVVGPIKQIEALQKKGYPLAYVGDVV 240
           DLSPAPDAWSRPDIPLHA AMLK AR+GI PD+ GV GP+KQIE ++ +G+P+AYVGDVV
Sbjct: 181 DLSPAPDAWSRPDIPLHALAMLKMARDGIVPDEQGVTGPMKQIETMRGEGFPIAYVGDVV 240

Query: 241 GTGSSRKSATNSVLWFMGDDIPNVPNKRGGGLCLGGKIAPIFFNTMEDAGALPIEVDVSN 300
           GTGSSRKSATNSVLWF GDD+PNVPNKR GG C G KIAPIF+NTMEDAGALPIE DVSN
Sbjct: 241 GTGSSRKSATNSVLWFFGDDVPNVPNKRAGGFCFGNKIAPIFYNTMEDAGALPIEFDVSN 300

Query: 301 LNMGDVIDVYPYKGEVRNHETGELLATFELKTDVLIDEVRAGGRIPLIIGRGLTTKAREA 360
           ++MGDVID+YP+ G+V  H T E+L TFE+KT VL+DEVRAGGRIPLIIGRGLT KAR  
Sbjct: 301 MHMGDVIDLYPHAGKVCKHGTDEVLTTFEMKTPVLLDEVRAGGRIPLIIGRGLTEKARAE 360

Query: 361 LGLPHSDVFRQAKDVAESSRGFSLAQKMVGRACGV---KGIRPGAYCEPKMTSVGSQDTT 417
           LGL  +D+F+  +  A S++GF+LAQKMVG+ACG+   +G+RPG YCEPKMT+VGSQDTT
Sbjct: 361 LGLGPTDLFKLPEPPAASTKGFTLAQKMVGKACGLAEGQGVRPGTYCEPKMTTVGSQDTT 420

Query: 418 GPMTRDELKDLACLGFSADLVMQSFCHTAAYPKPVDVTTHHTLPDFIMNRGGVSLRPGDG 477
           GPMTRDELKDLACLGFSADLVMQSFCHTAAYPKP+DVTTHHTLPDFI  RGGVSLRPGDG
Sbjct: 421 GPMTRDELKDLACLGFSADLVMQSFCHTAAYPKPIDVTTHHTLPDFIRTRGGVSLRPGDG 480

Query: 478 VIHSWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVRFK 537
           +IHSWLNRMLLPDTVGTGGDSHTRFP+GISFPAGSGLVAFAAATGVMPLDMPES+LVRFK
Sbjct: 481 IIHSWLNRMLLPDTVGTGGDSHTRFPMGISFPAGSGLVAFAAATGVMPLDMPESILVRFK 540

Query: 538 GKMQPGITLRDLVHAIPLYAIKQGLLTVEKKGKKNIFSGRILEIEGLPDLKVEQAFELTD 597
           GK+QPG+TLRDLVHAIP YAI++GLLTVEKKGK N FSGRILEIEGL +L VEQAFEL+D
Sbjct: 541 GKLQPGVTLRDLVHAIPYYAIQKGLLTVEKKGKVNAFSGRILEIEGLDELTVEQAFELSD 600

Query: 598 ASAERSAAGCTIKLNKEPIVEYLTSNIVLLKWMIAEGYGDRRTLERRIQGMEKWLADPQL 657
           ASAERSAAGCTIKL ++ I EYL SNI LL+WMI+EGYGD RT+ERR Q ME WLA+PQL
Sbjct: 601 ASAERSAAGCTIKLPEKAIAEYLQSNITLLRWMISEGYGDARTMERRAQAMEAWLANPQL 660

Query: 658 LEADADAEYAAVIDIDLADIKEPILCAPNDPDDARLLSDVQGEKIDEVFIGSCMTNIGHF 717
           + AD DAEYA +I+IDLA+I EPILCAPNDPDDARLLS V GEKIDEVFIGSCMTNIGHF
Sbjct: 661 MSADKDAEYAEIIEIDLAEINEPILCAPNDPDDARLLSSVAGEKIDEVFIGSCMTNIGHF 720

Query: 718 RAAGKLLDNHKGQLPTRLWVAPPTRMDAAQLTEEGYYSVFGKSGARIEIPGCSLCMGNQA 777
           RAAGKLL+   G LPTRLW++PPT+MD  QLTEEGYY ++GK+GAR+E+PGCSLCMGNQA
Sbjct: 721 RAAGKLLEKVDGSLPTRLWLSPPTKMDQHQLTEEGYYEIYGKAGARLEMPGCSLCMGNQA 780

Query: 778 RVADGATVVSTSTRNFPNRLGTGANVFLASAELAAVAALIGKLPTPEEYQTYVAQVDKTA 837
           RV   ATVVSTSTRNFPNRLG GANV+LASAELAAVA++IGKLPT EEY  Y   +D  A
Sbjct: 781 RVEAKATVVSTSTRNFPNRLGDGANVYLASAELAAVASIIGKLPTVEEYMVYAKDIDSMA 840

Query: 838 VDTYRYLNFDQLSQYTEKA 856
            D YRYL+FDQ++++ 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: 2207
Number of extensions: 85
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