GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acn in Marinobacter adhaerens HP15

Align aconitate hydratase (EC 4.2.1.3) (characterized)
to candidate GFF2253 HP15_2203 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase

Query= BRENDA::P36683
         (865 letters)



>FitnessBrowser__Marino:GFF2253
          Length = 864

 Score = 1269 bits (3284), Expect = 0.0
 Identities = 620/859 (72%), Positives = 720/859 (83%), Gaps = 4/859 (0%)

Query: 1   MLEEYRKHVAERAAEGIAPKPLDANQMAALVELLKNPPAGEEEFLLDLLTNRVPPGVDEA 60
           MLE YR+HVAER A GI PKPL+A Q AALV+LLKNPPAGEE+ L+ LL NRVPPGVDEA
Sbjct: 1   MLEAYREHVAEREALGIPPKPLNAEQTAALVDLLKNPPAGEEDTLVYLLENRVPPGVDEA 60

Query: 61  AYVKAGFLAAIAKGEAKSPLLTPEKAIELLGTMQGGYNIHPLIDALDDAKLAPIAAKALS 120
           AYVKA FL AI KGEA SPLL    A++LLG MQGGYNI  L+D LDD++LA +A + L 
Sbjct: 61  AYVKAAFLTAIVKGEASSPLLDKPTAVKLLGMMQGGYNIATLVDLLDDSELAELAGEQLK 120

Query: 121 HTLLMFDNFYDVEEKAKAGNEYAKQVMQSWADAEWFLNRPALAEKLTVTVFKVTGETNTD 180
            TLLMFD F DV+EK  AGN  A+ V++SWA+ EWF N+  + E   + VFKVTGETNTD
Sbjct: 121 RTLLMFDAFNDVKEKMDAGNPVARAVIESWANGEWFTNKKKVPESTKMVVFKVTGETNTD 180

Query: 181 DLSPAPDAWSRPDIPLHALAMLKNAREGIEPDQPGVVGPIKQIEALQQKGFPLAYVGDVV 240
           DLSPAPDAWSRPDIPLHA A  K  R+G++P++PGV GP+ QI+ ++ KG P+A+VGDVV
Sbjct: 181 DLSPAPDAWSRPDIPLHARAAYKMERDGLKPEEPGVTGPMSQIDEIKAKGLPVAFVGDVV 240

Query: 241 GTGSSRKSATNSVLWFMGDDIPHVPNKRGGGLCLGGKIAPIFFNTMEDAGALPIEVDVSN 300
           GTGSSRKSATNSVLWF GDDIP VPNKR GG+C+G K+APIFFNTMEDAGAL  E  V +
Sbjct: 241 GTGSSRKSATNSVLWFFGDDIPGVPNKRAGGVCIGNKVAPIFFNTMEDAGALVFEAPVDD 300

Query: 301 LNMGDVIDVYPYKGEVRNHETGELLATFELKTDVLIDEVRAGGRIPLIIGRGLTTKAREA 360
           +NMGDVI++ PY G++ N E GE ++ F+ K+DV++DEV+AGGRIPLIIGRGLT KAR A
Sbjct: 301 MNMGDVIEIRPYDGKILN-EAGETISEFKFKSDVILDEVQAGGRIPLIIGRGLTAKARTA 359

Query: 361 LGLPHSDVFRQAKDVAESDRGFSLAQKMVGRACGV---KGIRPGAYCEPKMTSVGSQDTT 417
           LG+  +D+FR  KD     +GF+LAQKMVG+ACG+   KG+RP  YCEP MT+VGSQDTT
Sbjct: 360 LGMGATDLFRLPKDPEAGTKGFTLAQKMVGKACGLEEGKGVRPNTYCEPHMTTVGSQDTT 419

Query: 418 GPMTRDELKDLACLGFSADLVMQSFCHTAAYPKPVDVNTHHTLPDFIMNRGGVSLRPGDG 477
           GPMTRDELKDLACLGF ADLVMQSFCHTAAYPKPVDV   HT+PDFI  RGGVSLRPGDG
Sbjct: 420 GPMTRDELKDLACLGFQADLVMQSFCHTAAYPKPVDVEMQHTMPDFIRTRGGVSLRPGDG 479

Query: 478 VIHSWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVRFK 537
           +IHSWLNRMLLPDTVGTGGDSHTRFP+GISFPAGSGLVAFAAATGVMPLDMPESVLVRFK
Sbjct: 480 IIHSWLNRMLLPDTVGTGGDSHTRFPMGISFPAGSGLVAFAAATGVMPLDMPESVLVRFK 539

Query: 538 GKMQPGITLRDLVHAIPLYAIKQGLLTVEKKGKKNIFSGRILEIEGLPDLKVEQAFELTD 597
           G+MQPGITLRDLVHAIPLY IKQG+LTVEKKGK N FSGRILEIEGL  L VEQAFEL+D
Sbjct: 540 GEMQPGITLRDLVHAIPLYGIKQGMLTVEKKGKINEFSGRILEIEGLEHLTVEQAFELSD 599

Query: 598 ASAERSAAGCTIKLNKEPIIEYLNSNIVLLKWMIAEGYGDRRTLERRIQGMEKWLANPEL 657
           ASAERSAAGCTI L+++ + EYL SNI +L+WMIAEGYGD RTLERR Q ME+WLA+P+L
Sbjct: 600 ASAERSAAGCTINLSEDSVAEYLRSNITMLRWMIAEGYGDPRTLERRAQQMEEWLADPKL 659

Query: 658 LEADADAEYAAVIDIDLADIKEPILCAPNDPDDARPLSAVQGEKIDEVFIGSCMTNIGHF 717
           + AD DAEYA VI+IDLADIKEPI+C PNDPDDA+ LS V G+K+DEVFIGSCMTNIGHF
Sbjct: 660 MRADKDAEYAHVIEIDLADIKEPIVCCPNDPDDAKFLSEVAGDKVDEVFIGSCMTNIGHF 719

Query: 718 RAAGKLLDAHKGQLPTRLWVAPPTRMDAAQLTEEGYYSVFGKSGARIEIPGCSLCMGNQA 777
           RAAGKLL+ HKG L TRLW++PPT+MD AQL EEGY++ +G +G R E+PGCSLCMGNQA
Sbjct: 720 RAAGKLLEQHKGPLSTRLWMSPPTKMDQAQLMEEGYFNTYGTAGVRTEMPGCSLCMGNQA 779

Query: 778 RVADGATVVSTSTRNFPNRLGTGANVFLASAELAAVAALIGKLPTPEEYQTYVAQVDKTA 837
           RVA  +TV+STSTRNFPNRLG GANV+L SAELAAV A++GKLP+P EY  Y   ++  +
Sbjct: 780 RVAPKSTVLSTSTRNFPNRLGDGANVYLTSAELAAVGAVLGKLPSPAEYMEYAKDLNSMS 839

Query: 838 VDTYRYLNFNQLSQYTEKA 856
            + Y+YLNF+Q+  YT+KA
Sbjct: 840 KEIYKYLNFDQMENYTKKA 858


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: 2088
Number of extensions: 72
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: 864
Length adjustment: 42
Effective length of query: 823
Effective length of database: 822
Effective search space:   676506
Effective search space used:   676506
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.

Links

Downloads

Related tools

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