GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acn in Shewanella halifaxensis HAW-EB4

Align aconitate hydratase (EC 4.2.1.3) (characterized)
to candidate WP_012275611.1 SHAL_RS02455 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase

Query= BRENDA::P36683
         (865 letters)



>NCBI__GCF_000019185.1:WP_012275611.1
          Length = 865

 Score = 1431 bits (3705), Expect = 0.0
 Identities = 697/865 (80%), Positives = 783/865 (90%)

Query: 1   MLEEYRKHVAERAAEGIAPKPLDANQMAALVELLKNPPAGEEEFLLDLLTNRVPPGVDEA 60
           MLE YRKHVAERA+EG+ PKPLDA Q+A LVEL+KNPPAGEE F+LDLL NR+PPGVDEA
Sbjct: 1   MLEAYRKHVAERASEGVVPKPLDAQQVAQLVELVKNPPAGEEAFILDLLENRIPPGVDEA 60

Query: 61  AYVKAGFLAAIAKGEAKSPLLTPEKAIELLGTMQGGYNIHPLIDALDDAKLAPIAAKALS 120
           AYVKAGFL A+AK E  SP+L+ ++A+ELLGTMQGGYNI PLI  LD+   AP+A KALS
Sbjct: 61  AYVKAGFLDAVAKCEIASPILSSQRAVELLGTMQGGYNIEPLIAQLDNDAQAPLAVKALS 120

Query: 121 HTLLMFDNFYDVEEKAKAGNEYAKQVMQSWADAEWFLNRPALAEKLTVTVFKVTGETNTD 180
           HTLLMFD+F+DV +K +AGN+YAKQV+ +WADA+WFL+RP LAEK+++TVFKV+GETNTD
Sbjct: 121 HTLLMFDSFHDVVDKMQAGNDYAKQVVHAWADAKWFLSRPKLAEKISLTVFKVSGETNTD 180

Query: 181 DLSPAPDAWSRPDIPLHALAMLKNAREGIEPDQPGVVGPIKQIEALQQKGFPLAYVGDVV 240
           DLSPAPDAWSRPDIPLHALAMLKNAR+GI PD+ GVVGPIK+IE+L+ KGFPL YVGDVV
Sbjct: 181 DLSPAPDAWSRPDIPLHALAMLKNARDGIVPDEAGVVGPIKEIESLKTKGFPLVYVGDVV 240

Query: 241 GTGSSRKSATNSVLWFMGDDIPHVPNKRGGGLCLGGKIAPIFFNTMEDAGALPIEVDVSN 300
           GTGSSRKSATNSVLWFMGDDIP+VPNKR GG CLGGKIAPIFFNTMEDAGALPIE+DVS 
Sbjct: 241 GTGSSRKSATNSVLWFMGDDIPNVPNKRAGGFCLGGKIAPIFFNTMEDAGALPIELDVSK 300

Query: 301 LNMGDVIDVYPYKGEVRNHETGELLATFELKTDVLIDEVRAGGRIPLIIGRGLTTKAREA 360
           + MGDVID+YPY+G V+ H T E+++ F LKTDVL+DEVRAGGRIPLIIGRGLT +ARE 
Sbjct: 301 MEMGDVIDIYPYEGIVKRHGTDEVISQFSLKTDVLMDEVRAGGRIPLIIGRGLTDRARET 360

Query: 361 LGLPHSDVFRQAKDVAESDRGFSLAQKMVGRACGVKGIRPGAYCEPKMTSVGSQDTTGPM 420
           L L  S  F + KDVA++ +GF+LAQKMVG+ACGV GIRPG YCEPKMTSVGSQDTTGPM
Sbjct: 361 LNLEASTEFVRPKDVADTGKGFTLAQKMVGKACGVTGIRPGQYCEPKMTSVGSQDTTGPM 420

Query: 421 TRDELKDLACLGFSADLVMQSFCHTAAYPKPVDVNTHHTLPDFIMNRGGVSLRPGDGVIH 480
           TRDELKDLACLGFSADL MQSFCHTAAYPKPVDVNTHHTLPDFIMNRGGVSLRPGDGVIH
Sbjct: 421 TRDELKDLACLGFSADLTMQSFCHTAAYPKPVDVNTHHTLPDFIMNRGGVSLRPGDGVIH 480

Query: 481 SWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVRFKGKM 540
           SWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPES+LVRFKG+M
Sbjct: 481 SWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESILVRFKGEM 540

Query: 541 QPGITLRDLVHAIPLYAIKQGLLTVEKKGKKNIFSGRILEIEGLPDLKVEQAFELTDASA 600
           QPGITLRDLVHAIP  AI+ GLLTVEKKGK N FSGR+LEIEGL  LKVEQAFEL+DASA
Sbjct: 541 QPGITLRDLVHAIPHKAIEMGLLTVEKKGKINAFSGRVLEIEGLEQLKVEQAFELSDASA 600

Query: 601 ERSAAGCTIKLNKEPIIEYLNSNIVLLKWMIAEGYGDRRTLERRIQGMEKWLANPELLEA 660
           ERSAAGCTIKL+KEPIIEYLNSNIV+LKWMI+EGYGDRRT+ERRI  M++WLA PEL+EA
Sbjct: 601 ERSAAGCTIKLDKEPIIEYLNSNIVMLKWMISEGYGDRRTIERRITAMQEWLATPELMEA 660

Query: 661 DADAEYAAVIDIDLADIKEPILCAPNDPDDARPLSAVQGEKIDEVFIGSCMTNIGHFRAA 720
           D+DAEYA VI+IDL +IKEPILCAPNDPDDA  LS+V   KIDEVF+GSCMTNIGHFRA 
Sbjct: 661 DSDAEYAEVIEIDLNEIKEPILCAPNDPDDAILLSSVVNTKIDEVFVGSCMTNIGHFRAT 720

Query: 721 GKLLDAHKGQLPTRLWVAPPTRMDAAQLTEEGYYSVFGKSGARIEIPGCSLCMGNQARVA 780
           GK+LD     LPTRLW+APPT+MD  QLTEEGYY++FG+ GARIEIPGCSLCMGNQARVA
Sbjct: 721 GKMLDKFASTLPTRLWIAPPTKMDRDQLTEEGYYAIFGRVGARIEIPGCSLCMGNQARVA 780

Query: 781 DGATVVSTSTRNFPNRLGTGANVFLASAELAAVAALIGKLPTPEEYQTYVAQVDKTAVDT 840
           +GATVVSTSTRNFPNRLGTGANV+LASAELA+VAAL+G+LP+P+EYQTY  ++D TA DT
Sbjct: 781 EGATVVSTSTRNFPNRLGTGANVYLASAELASVAALLGRLPSPDEYQTYAKELDATAADT 840

Query: 841 YRYLNFNQLSQYTEKADGVIFQTAV 865
           YRYL+F++++ YT KAD VIFQTAV
Sbjct: 841 YRYLSFDKIASYTAKADEVIFQTAV 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: 2136
Number of extensions: 75
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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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:

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:

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:

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:

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