Alignments for a candidate for acn in Halomonas desiderata SP1

GapMind for catabolism of small carbon sources

Alignments for a candidate for acn in Halomonas desiderata SP1

Align aconitate hydratase (EC 4.2.1.3) (characterized)
to candidate WP_086509646.1 BZY95_RS09205 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase

Query= BRENDA::P36683
         (865 letters)



>NCBI__GCF_002151265.1:WP_086509646.1
          Length = 867

 Score = 1370 bits (3547), Expect = 0.0
 Identities = 671/861 (77%), Positives = 752/861 (87%), Gaps = 1/861 (0%)

Query: 1   MLEEYRKHVAERAAEGIAPKPLDANQMAALVELLKNPPAGEEEFLLDLLTNRVPPGVDEA 60
           MLE YR+HV ERAAEG+ PKPL+A Q AALVELLKNPPAGEEEF+LDLLTNR+PPGVDEA
Sbjct: 1   MLEAYRQHVEERAAEGVPPKPLNAEQAAALVELLKNPPAGEEEFVLDLLTNRIPPGVDEA 60

Query: 61  AYVKAGFLAAIAKGEAKSPLLTPEKAIELLGTMQGGYNIHPLIDALDDAKLAPIAAKALS 120
           AYVKAGFL AI KGEA+SPL+    A++LLGTMQGGYNI  L++ LDDA+LA  A + L 
Sbjct: 61  AYVKAGFLTAITKGEAQSPLVDKVHAVKLLGTMQGGYNIATLVELLDDAELAKEAGEQLK 120

Query: 121 HTLLMFDNFYDVEEKAKAGNEYAKQVMQSWADAEWFLNRPALAEKLTVTVFKVTGETNTD 180
           HTLLMFD F+DVEE+AKAGN  AK VMQSWA+AEWFL++PALAEK+T+TVFKV GETNTD
Sbjct: 121 HTLLMFDAFHDVEERAKAGNAVAKDVMQSWAEAEWFLSKPALAEKITLTVFKVPGETNTD 180

Query: 181 DLSPAPDAWSRPDIPLHALAMLKNAREGIEPDQPGVVGPIKQIEALQQKGFPLAYVGDVV 240
           DLSPAPDAWSRPDIPLHA AMLKN REGI P+ PG  GP+KQIE ++ KG+P+AYVGDVV
Sbjct: 181 DLSPAPDAWSRPDIPLHANAMLKNEREGIVPEVPGTTGPLKQIEEVKAKGYPVAYVGDVV 240

Query: 241 GTGSSRKSATNSVLWFMGDDIPHVPNKRGGGLCLGGKIAPIFFNTMEDAGALPIEVDVSN 300
           GTGSSRKSATNSVLWF GDDIP+VPNKR GG C GGKIAPIFFNTMEDAGALP+E+DVS 
Sbjct: 241 GTGSSRKSATNSVLWFFGDDIPNVPNKRAGGFCFGGKIAPIFFNTMEDAGALPVEMDVSK 300

Query: 301 LNMGDVIDVYPYKGEVRNHETGELLATFELKTDVLIDEVRAGGRIPLIIGRGLTTKAREA 360
           L MGDVIDVYPY+G+V  H T E+L TFELKT V++DEVRAGGRIPLIIGRGLT KARE+
Sbjct: 301 LEMGDVIDVYPYEGKVCKHGTDEVLTTFELKTQVILDEVRAGGRIPLIIGRGLTGKARES 360

Query: 361 LGLPHSDVFRQAKDVAESDRGFSLAQKMVGRACGVKGIRPGAYCEPKMTSVGSQDTTGPM 420
           LGL  SDVFR  +   ++ +GF+LAQKMVG+ACG+ G+RPG YCEPKMT+VGSQDTTGPM
Sbjct: 361 LGLAPSDVFRLPEQPKDTGKGFTLAQKMVGKACGMAGVRPGMYCEPKMTTVGSQDTTGPM 420

Query: 421 TRDELKDLACLGFSADLVMQSFCHTAAYPKPVDVNTHHTLPDFIMNRGGVSLRPGDGVIH 480
           TRDELKDLACLGF ADLVMQSFCHTAAYPKPVDV THHTLPDFIMNRGGVSLRPGDG+IH
Sbjct: 421 TRDELKDLACLGFQADLVMQSFCHTAAYPKPVDVETHHTLPDFIMNRGGVSLRPGDGIIH 480

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

Query: 541 QPGITLRDLVHAIPLYAIKQGLLTVEKKGKKNIFSGRILEIEGLPDLKVEQAFELTDASA 600
           QPG+TLRDLVHAIP YAIKQGLLTV K GKKN FSGR+LEIEGL DL VEQAFEL+DASA
Sbjct: 541 QPGVTLRDLVHAIPYYAIKQGLLTVAKAGKKNAFSGRVLEIEGLEDLTVEQAFELSDASA 600

Query: 601 ERSAAGCTIKLNKEPIIEYLNSNIVLLKWMIAEGYGDRRTLERRIQGMEKWLANPELLEA 660
           ERSAAGCTI L +  + EYL SNI LLKWMIA GYGD+RT+ERRI  ME+WLANP L+ A
Sbjct: 601 ERSAAGCTITLGEASVTEYLKSNITLLKWMIANGYGDKRTIERRILAMEEWLANPSLMRA 660

Query: 661 DADAEYAAVIDIDLADIKEPILCAPNDPDDARPLSAVQGEKIDEVFIGSCMTNIGHFRAA 720
           D DAEYA VI+IDL ++KEP+LCAPNDPDDAR LS V GEKIDEVFIGSCMTNIGHFRAA
Sbjct: 661 DKDAEYAEVIEIDLDELKEPVLCAPNDPDDARLLSEVAGEKIDEVFIGSCMTNIGHFRAA 720

Query: 721 GKLLDAH-KGQLPTRLWVAPPTRMDAAQLTEEGYYSVFGKSGARIEIPGCSLCMGNQARV 779
           GKLL+    G L TRLW+APPT+MD  QLTEEGYY ++G++GAR+E+PGCSLCMGNQARV
Sbjct: 721 GKLLEKQPAGSLKTRLWLAPPTKMDQHQLTEEGYYGIYGRAGARMEMPGCSLCMGNQARV 780

Query: 780 ADGATVVSTSTRNFPNRLGTGANVFLASAELAAVAALIGKLPTPEEYQTYVAQVDKTAVD 839
           A  +TVVSTSTRNFPNRLG GANV+LASAELAAVAA+ G+LP+ EEYQ Y+ + D  A +
Sbjct: 781 AAKSTVVSTSTRNFPNRLGDGANVYLASAELAAVAAVEGRLPSVEEYQRYMGEFDAMAGE 840

Query: 840 TYRYLNFNQLSQYTEKADGVI 860
            YRY+NF+++ +Y   A  VI
Sbjct: 841 IYRYMNFHEIEEYQNAASNVI 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: 2191
Number of extensions: 73
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: 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