GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acn in Cupriavidus basilensis 4G11

Align aconitate hydratase (EC 4.2.1.3) (characterized)
to candidate RR42_RS23515 RR42_RS23515 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase

Query= BRENDA::P36683
         (865 letters)



>FitnessBrowser__Cup4G11:RR42_RS23515
          Length = 861

 Score = 1280 bits (3312), Expect = 0.0
 Identities = 637/862 (73%), Positives = 731/862 (84%), Gaps = 6/862 (0%)

Query: 1   MLEEYRKHVAERAAEGIAPKPLDANQMAALVELLKNPPAGEEEFLLDLLTNRVPPGVDEA 60
           MLE YR HVAERAA GI P PL A Q A L+ELLK+PPAGEE+ L+DL+T+RVP GVD+A
Sbjct: 1   MLENYRAHVAERAALGIPPLPLTAKQTAELIELLKSPPAGEEQVLVDLITHRVPAGVDDA 60

Query: 61  AYVKAGFLAAIAKGEAKSPLLTPEKAIELLGTMQGGYNIHPLIDALDDAKLAPIAAKALS 120
           A VKA +LAA+A G+    L++  KA ELLGTM GGYNI PLI+ LDDA++ P+AA+AL 
Sbjct: 61  AKVKASYLAAVALGKEACALISRAKAAELLGTMLGGYNISPLIELLDDAEIGPVAAEALK 120

Query: 121 HTLLMFDNFYDVEEKAKAGNEYAKQVMQSWADAEWFLNRPALAEKLTVTVFKVTGETNTD 180
            TLLMFD F+DV+EKA  GN  AK V+QSWADAEWF +RP + + LTVTVFKVTGETNTD
Sbjct: 121 KTLLMFDAFHDVKEKADKGNAIAKSVLQSWADAEWFTSRPEVPQSLTVTVFKVTGETNTD 180

Query: 181 DLSPAPDAWSRPDIPLHALAMLKNAREGIEPDQPGVVGPIKQIEALQQKGFPLAYVGDVV 240
           DLSPAPDA +RPDIPLHALAMLKNAR GI P++ G  GP+K IE+L++KG  +AYVGDVV
Sbjct: 181 DLSPAPDATTRPDIPLHALAMLKNARPGITPEEDGKRGPVKFIESLKEKGNLVAYVGDVV 240

Query: 241 GTGSSRKSATNSVLWFMGDDIPHVPNKRGGGLCLGGKIAPIFFNTMEDAGALPIEVDVSN 300
           GTGSSRKSATNSVLWF G+DIP VPNKR GG+CLG KIAPIF+NTMEDAGALPIE+DVS 
Sbjct: 241 GTGSSRKSATNSVLWFTGEDIPFVPNKRFGGVCLGSKIAPIFYNTMEDAGALPIELDVSQ 300

Query: 301 LNMGDVIDVYPYKGEVRNHETGELLATFELKTDVLIDEVRAGGRIPLIIGRGLTTKAREA 360
           + MGDV+++ PY G+   +  G+++A F +K+DVL DEVRAGGRIPLI+GRGLT KAREA
Sbjct: 301 MEMGDVVELRPYDGKALKN--GQVIAEFTVKSDVLFDEVRAGGRIPLIVGRGLTAKAREA 358

Query: 361 LGLPHSDVFRQAKDVAESDRGFSLAQKMVGRACGV---KGIRPGAYCEPKMTSVGSQDTT 417
           LGL  S +FR   + A++ RGF+LAQKMVGRACG+   KGIRPG YCEPKMTSVGSQDTT
Sbjct: 359 LGLAPSTLFRLPHNPADTGRGFTLAQKMVGRACGLPEGKGIRPGTYCEPKMTSVGSQDTT 418

Query: 418 GPMTRDELKDLACLGFSADLVMQSFCHTAAYPKPVDVNTHHTLPDFIMNRGGVSLRPGDG 477
           GPMTRDELKDLACLGFSADLVMQSFCHTAAYPKPVDV THHTLP FI  RGG+SLRPGDG
Sbjct: 419 GPMTRDELKDLACLGFSADLVMQSFCHTAAYPKPVDVKTHHTLPQFISTRGGISLRPGDG 478

Query: 478 VIHSWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVRFK 537
           VIHSWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVRFK
Sbjct: 479 VIHSWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVRFK 538

Query: 538 GKMQPGITLRDLVHAIPLYAIKQGLLTVEKKGKKNIFSGRILEIEGLPDLKVEQAFELTD 597
           GKMQPG+TLRDLV+AIPLYAIK GLLTV K+GKKNIFSGR+LEIEGLPDLKVEQAFEL+D
Sbjct: 539 GKMQPGVTLRDLVNAIPLYAIKSGLLTVAKQGKKNIFSGRVLEIEGLPDLKVEQAFELSD 598

Query: 598 ASAERSAAGCTIKLNKEPIIEYLNSNIVLLKWMIAEGYGDRRTLERRIQGMEKWLANPEL 657
           ASAERSAAGC+++LNKEPIIEY+NSNI LLKWMIAEGY D R+L RRIQ ME WLA+P+L
Sbjct: 599 ASAERSAAGCSVRLNKEPIIEYINSNITLLKWMIAEGYQDPRSLSRRIQAMEAWLADPKL 658

Query: 658 LEADADAEYAAVIDIDLADIKEPILCAPNDPDDARPLSAVQGEKIDEVFIGSCMTNIGHF 717
           LE DADAEYAAVI+IDLAD+ EPI+  PNDPDD + LS V G KIDEVFIGSCMTNIGHF
Sbjct: 659 LEPDADAEYAAVIEIDLADVHEPIVACPNDPDDVKTLSEVAGAKIDEVFIGSCMTNIGHF 718

Query: 718 RAAGKLLDAHKGQLPTRLWVAPPTRMDAAQLTEEGYYSVFGKSGARIEIPGCSLCMGNQA 777
           RAA KLL+  K  +P +LWVAPPT+MDA QLTEEG+Y VFG +GAR E+PGCSLCMGNQA
Sbjct: 719 RAASKLLEG-KRDIPVKLWVAPPTKMDAKQLTEEGHYGVFGTAGARTEMPGCSLCMGNQA 777

Query: 778 RVADGATVVSTSTRNFPNRLGTGANVFLASAELAAVAALIGKLPTPEEYQTYVAQVDKTA 837
           +V +GATV+STSTRNFPNRLG   NV+L SAELAA+ + +G++PT EEY + +  +    
Sbjct: 778 QVREGATVMSTSTRNFPNRLGKNTNVYLGSAELAAICSRLGRIPTKEEYMSDMGVLATNG 837

Query: 838 VDTYRYLNFNQLSQYTEKADGV 859
              Y+YLNF+++  +   AD V
Sbjct: 838 DQIYKYLNFDKIEDFKGVADTV 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: 2045
Number of extensions: 73
Number of successful extensions: 4
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: 861
Length adjustment: 42
Effective length of query: 823
Effective length of database: 819
Effective search space:   674037
Effective search space used:   674037
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 17 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