Alignments for a candidate for acn in Psychrobacter arcticus 273-4

GapMind for catabolism of small carbon sources

Alignments for a candidate for acn in Psychrobacter arcticus 273-4

Align aconitate hydratase (EC 4.2.1.3) (characterized)
to candidate WP_011280032.1 PSYC_RS03925 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase

Query= BRENDA::P36683
         (865 letters)



>NCBI__GCF_000012305.1:WP_011280032.1
          Length = 867

 Score = 1293 bits (3345), Expect = 0.0
 Identities = 631/861 (73%), Positives = 736/861 (85%), Gaps = 2/861 (0%)

Query: 1   MLEEYRKHVAERAAEGIAPKPLDANQMAALVELLKNPPAGEEEFLLDLLTNRVPPGVDEA 60
           MLE YRKHVAERA  GI P PL+  Q+  LVELLKNPPAGE+ FL+DLL NR+P GVD+A
Sbjct: 1   MLEAYRKHVAERAELGIVPLPLNEKQVVELVELLKNPPAGEDAFLMDLLENRIPAGVDQA 60

Query: 61  AYVKAGFLAAIAKGEAKSPLLTPEKAIELLGTMQGGYNIHPLIDALDDAKLAPIAAKALS 120
           AYVKA FLAAI KGEA SPLL+ +KA+++LGTMQGGYN+ PL+ ALDDA++A  AA AL 
Sbjct: 61  AYVKAAFLAAIVKGEATSPLLSKKKAVQILGTMQGGYNVQPLVAALDDAEVAQEAADALK 120

Query: 121 HTLLMFDNFYDVEEKAKAGNEYAKQVMQSWADAEWFLNRPALAEKLTVTVFKVTGETNTD 180
            TLL+FD F DV EKA+AGN  AK+V+QSWADAEWFL+R A+  K T T FKVTGETNTD
Sbjct: 121 KTLLVFDAFNDVTEKAEAGNTIAKEVVQSWADAEWFLSRDAVPAKTTYTTFKVTGETNTD 180

Query: 181 DLSPAPDAWSRPDIPLHALAMLKNAREGIEPDQPGVVGPIKQIEALQQKGFPLAYVGDVV 240
           DLSPA DAWSRPDIPLH+LAM KN+R+GI  D+ GVVG +KQIEAL++KG  LAYVGDVV
Sbjct: 181 DLSPAQDAWSRPDIPLHSLAMHKNSRDGIIADEEGVVGSMKQIEALKEKGHQLAYVGDVV 240

Query: 241 GTGSSRKSATNSVLWFMGDDIPHVPNKRGGGLCLGGKIAPIFFNTMEDAGALPIE-VDVS 299
           GTGSSRKSATNSVLW MGDDIP+VPNKRGGGL LG  IAPIFFNTMED+GALPI+ V+V 
Sbjct: 241 GTGSSRKSATNSVLWLMGDDIPNVPNKRGGGLVLGNNIAPIFFNTMEDSGALPIDGVNVD 300

Query: 300 NLNMGDVIDVYPYKGEVRNHETGELLATFELKTDVLIDEVRAGGRIPLIIGRGLTTKARE 359
           NLNMGDV D+YPY+G++  H++ E+L+TF+L +  L+DEVRAGGRIPLI+GRGLT +ARE
Sbjct: 301 NLNMGDVFDIYPYEGKITKHDSDEVLSTFKLNSPTLLDEVRAGGRIPLIVGRGLTNRARE 360

Query: 360 ALGLPHSDVFRQAKDVAESDRGFSLAQKMVGRACGVKGIRPGAYCEPKMTSVGSQDTTGP 419
            +GL HSDVF + ++  ++ +GF+LAQKMVG+ACG++G+RPG YCEPK+T+VGSQDTTGP
Sbjct: 361 YMGLSHSDVFAKPEEPVDTGKGFTLAQKMVGKACGMQGVRPGMYCEPKITTVGSQDTTGP 420

Query: 420 MTRDELKDLACLGFSADLVMQSFCHTAAYPKPVDVNTHHTLPDFIMNRGGVSLRPGDGVI 479
           MTRDELKDLACLGF ADLVMQSFCHTAAYPKPVDV T HTLPDFIMNRGGVSLRPGDG+I
Sbjct: 421 MTRDELKDLACLGFQADLVMQSFCHTAAYPKPVDVETQHTLPDFIMNRGGVSLRPGDGII 480

Query: 480 HSWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVRFKGK 539
           HSWLNRMLLPDTVGTGGDSHTRFP+GISFPAGSGLVAFAAATGVMPLDMPESV VRF G+
Sbjct: 481 HSWLNRMLLPDTVGTGGDSHTRFPMGISFPAGSGLVAFAAATGVMPLDMPESVRVRFIGE 540

Query: 540 MQPGITLRDLVHAIPLYAIKQGLLTVEKKGKKNIFSGRILEIEGLPDLKVEQAFELTDAS 599
            Q GITLRDLVHAIP  AIK+G LTV+KKGK N F+GRILEIEGL DL  EQAFEL+DAS
Sbjct: 541 RQAGITLRDLVHAIPYQAIKEGYLTVDKKGKINEFNGRILEIEGLEDLTAEQAFELSDAS 600

Query: 600 AERSAAGCTIKLNKEPIIEYLNSNIVLLKWMIAEGYGDRRTLERRIQGMEKWLANPELLE 659
           AERSAAGCTI L++  + EYLNSNI LLKWMI+EGYGD RT+ RR++ M++WLANP LL 
Sbjct: 601 AERSAAGCTITLSEASVTEYLNSNITLLKWMISEGYGDARTISRRVEQMQEWLANPSLLR 660

Query: 660 ADADAEYAAVIDIDLADIKEPILCAPNDPDDARPLSAVQGEKIDEVFIGSCMTNIGHFRA 719
           AD DAEYA  + ID+++IKEPILC PNDPDDA+ L+ V G+ IDEVFIGSCMTNIGHFRA
Sbjct: 661 ADEDAEYAIDMVIDMSEIKEPILCCPNDPDDAKTLADVAGDTIDEVFIGSCMTNIGHFRA 720

Query: 720 AGKLL-DAHKGQLPTRLWVAPPTRMDAAQLTEEGYYSVFGKSGARIEIPGCSLCMGNQAR 778
           AGKLL D   G L TRLW+APPT+MDA QL EEGYY+++ ++GAR E+PGCSLCMGNQAR
Sbjct: 721 AGKLLQDVPAGSLKTRLWIAPPTKMDARQLMEEGYYNIYAQAGARTEMPGCSLCMGNQAR 780

Query: 779 VADGATVVSTSTRNFPNRLGTGANVFLASAELAAVAALIGKLPTPEEYQTYVAQVDKTAV 838
           +A  +T VSTSTRNFPNRLG GANV+LASAELA+VAA++GKLPT EEYQ Y   +D    
Sbjct: 781 IAPNSTAVSTSTRNFPNRLGQGANVYLASAELASVAAVLGKLPTNEEYQQYAGMLDSMGE 840

Query: 839 DTYRYLNFNQLSQYTEKADGV 859
           + Y+Y+NF+++  YTE+AD +
Sbjct: 841 EVYQYMNFDRMESYTEEADKI 861


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: 2017
Number of extensions: 62
Number of successful extensions: 3
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: 867
Length adjustment: 42
Effective length of query: 823
Effective length of database: 825
Effective search space:   678975
Effective search space used:   678975
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