Alignments for a candidate for acn in Pseudoalteromonas arctica A 37-1-2

GapMind for catabolism of small carbon sources

Alignments for a candidate for acn in Pseudoalteromonas arctica A 37-1-2

Align aconitate hydratase (EC 4.2.1.3) (characterized)
to candidate WP_007579986.1 PARC_RS00910 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase

Query= BRENDA::P36683
         (865 letters)



>NCBI__GCF_000238395.3:WP_007579986.1
          Length = 865

 Score = 1396 bits (3614), Expect = 0.0
 Identities = 681/865 (78%), Positives = 763/865 (88%)

Query: 1   MLEEYRKHVAERAAEGIAPKPLDANQMAALVELLKNPPAGEEEFLLDLLTNRVPPGVDEA 60
           ML+EYRKHV ERAA GI P PLDA Q A L+EL+K PPAGEEEF+LDL   R+P GVD+A
Sbjct: 1   MLQEYRKHVEERAALGIVPAPLDAQQTADLIELIKTPPAGEEEFILDLFIQRIPAGVDDA 60

Query: 61  AYVKAGFLAAIAKGEAKSPLLTPEKAIELLGTMQGGYNIHPLIDALDDAKLAPIAAKALS 120
           AY+KAGFLAA+AKGE  SPL++ EKA ELLGTM GGYNI P+ID LDD  LAPI  K LS
Sbjct: 61  AYIKAGFLAAVAKGETNSPLVSKEKAAELLGTMLGGYNIAPMIDLLDDETLAPIVVKGLS 120

Query: 121 HTLLMFDNFYDVEEKAKAGNEYAKQVMQSWADAEWFLNRPALAEKLTVTVFKVTGETNTD 180
           +TLLMFD FYDVEEKAKAGN +AKQ+++SWA+AEWF N+PA+AEK++VTVFKVTGETNTD
Sbjct: 121 NTLLMFDAFYDVEEKAKAGNTFAKQIIESWANAEWFTNKPAVAEKISVTVFKVTGETNTD 180

Query: 181 DLSPAPDAWSRPDIPLHALAMLKNAREGIEPDQPGVVGPIKQIEALQQKGFPLAYVGDVV 240
           DLSPAPDAWSRPDIPLHALAMLK  R+GI PD+ G VGPI QIE L+ KG PLAYVGDVV
Sbjct: 181 DLSPAPDAWSRPDIPLHALAMLKIERDGITPDKAGEVGPITQIEELKTKGLPLAYVGDVV 240

Query: 241 GTGSSRKSATNSVLWFMGDDIPHVPNKRGGGLCLGGKIAPIFFNTMEDAGALPIEVDVSN 300
           GTGSSRKSATNSVLWFMGDDIP VPNKR GG+CLG KIAPIFFNTMED+GALPIE++V  
Sbjct: 241 GTGSSRKSATNSVLWFMGDDIPFVPNKRVGGVCLGNKIAPIFFNTMEDSGALPIELNVDE 300

Query: 301 LNMGDVIDVYPYKGEVRNHETGELLATFELKTDVLIDEVRAGGRIPLIIGRGLTTKAREA 360
           LNMG+ ID+YPY+G V+ H T ++++TFELK+DV++DEVRAGGRIPLIIGRGLT KAR +
Sbjct: 301 LNMGEQIDIYPYEGVVKQHGTDKVISTFELKSDVILDEVRAGGRIPLIIGRGLTDKARTS 360

Query: 361 LGLPHSDVFRQAKDVAESDRGFSLAQKMVGRACGVKGIRPGAYCEPKMTSVGSQDTTGPM 420
           LGL  +D F+       SD+GF+LAQKMVG+AC V GIRPG YCEPKMT+VGSQDTTGPM
Sbjct: 361 LGLGATDTFKVPTATEVSDKGFTLAQKMVGKACNVAGIRPGQYCEPKMTTVGSQDTTGPM 420

Query: 421 TRDELKDLACLGFSADLVMQSFCHTAAYPKPVDVNTHHTLPDFIMNRGGVSLRPGDGVIH 480
           TRDELKDLACLGFSADL MQSFCHT+AYPKP+DV+THHTLPDFIMNRGGVSLRPGDG+IH
Sbjct: 421 TRDELKDLACLGFSADLTMQSFCHTSAYPKPIDVSTHHTLPDFIMNRGGVSLRPGDGIIH 480

Query: 481 SWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVRFKGKM 540
           SWLNRMLLPDTVGTGGDSHTRFP+GISFPAGSG VAFAAATGVMPLDMPES+LVRFKG+M
Sbjct: 481 SWLNRMLLPDTVGTGGDSHTRFPLGISFPAGSGAVAFAAATGVMPLDMPESILVRFKGEM 540

Query: 541 QPGITLRDLVHAIPLYAIKQGLLTVEKKGKKNIFSGRILEIEGLPDLKVEQAFELTDASA 600
           QPGITLRDLVHAIP Y IKQGLLTVEKKGK N FSGR+LEIEG+  L VEQAFEL+DASA
Sbjct: 541 QPGITLRDLVHAIPYYGIKQGLLTVEKKGKINEFSGRVLEIEGVEHLTVEQAFELSDASA 600

Query: 601 ERSAAGCTIKLNKEPIIEYLNSNIVLLKWMIAEGYGDRRTLERRIQGMEKWLANPELLEA 660
           ERSAAGCT+KL+KE I EYL SNIV+LKWMI+EGYGD RT+ERRI  M+ WLANPEL+EA
Sbjct: 601 ERSAAGCTVKLSKESISEYLESNIVMLKWMISEGYGDVRTIERRITAMQDWLANPELMEA 660

Query: 661 DADAEYAAVIDIDLADIKEPILCAPNDPDDARPLSAVQGEKIDEVFIGSCMTNIGHFRAA 720
           DADAEY  +++IDLA+IKEP+LCAPNDPDDAR LS V GEKIDEVFIGSCMTNIGHFRAA
Sbjct: 661 DADAEYKHIVEIDLAEIKEPVLCAPNDPDDARLLSDVAGEKIDEVFIGSCMTNIGHFRAA 720

Query: 721 GKLLDAHKGQLPTRLWVAPPTRMDAAQLTEEGYYSVFGKSGARIEIPGCSLCMGNQARVA 780
           GKLLD  KGQLPT+LWVAPPT+MD  QLTEEGYY +FG+ GARIE PGCSLCMGNQARVA
Sbjct: 721 GKLLDGFKGQLPTQLWVAPPTKMDKDQLTEEGYYGIFGRVGARIETPGCSLCMGNQARVA 780

Query: 781 DGATVVSTSTRNFPNRLGTGANVFLASAELAAVAALIGKLPTPEEYQTYVAQVDKTAVDT 840
           D ATVVSTSTRNFPNRLG GANVFLAS+ELAA+AA+IGKLPT  EYQ Y A+++ TA DT
Sbjct: 781 DKATVVSTSTRNFPNRLGNGANVFLASSELAAIAAIIGKLPTVAEYQEYAAKINATASDT 840

Query: 841 YRYLNFNQLSQYTEKADGVIFQTAV 865
           YRYLNF+++  YT+KAD VI Q AV
Sbjct: 841 YRYLNFHRMPAYTKKADNVIIQQAV 865


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: 2110
Number of extensions: 83
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: 865
Length adjustment: 42
Effective length of query: 823
Effective length of database: 823
Effective search space:   677329
Effective search space used:   677329
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