GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acnD in Burkholderia phytofirmans PsJN

Align 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) (EC 4.2.1.117) (characterized)
to candidate BPHYT_RS33980 BPHYT_RS33980 aconitate hydratase

Query= BRENDA::Q8EJW3
         (867 letters)



>FitnessBrowser__BFirm:BPHYT_RS33980
          Length = 905

 Score =  646 bits (1666), Expect = 0.0
 Identities = 352/861 (40%), Positives = 520/861 (60%), Gaps = 45/861 (5%)

Query: 37  KLPYTSRVLAENLVRRCEPEMLTAS-LKQIIESKQEL----DFPWFPARVVCHDILGQTA 91
           +LP + R++ E+++R  + + +    ++Q+   K       + P+  +RVV  D  G   
Sbjct: 37  RLPVSIRIVLESVLRNYDGKKIAEEHIEQLANWKPTAARVDEIPFVVSRVVLQDFTGVPL 96

Query: 92  LVDLAGLRDAIAAKGGDPAQVNPVVPTQLIVDHSLAVEYGGFDKDAFAKNRAIEDRRNED 151
           L D+A +R      G DP  + P+VP  L+VDHS+ +++   +K+A   N  +E +RN +
Sbjct: 97  LADIAAMRGVAKHMGKDPKSIEPLVPVDLVVDHSVQIDHFR-EKNALDLNMKLEFQRNNE 155

Query: 152 RFHFINWTQKAFKNIDVIPQGNGIMHQINLERMSPVIHAR----NGVAFPDTLVGTDSHT 207
           R+ F+ W  +AF    V+P G GI+HQ+NLE ++  +H +    + V +PD+LVGTDSHT
Sbjct: 156 RYQFMKWGMQAFDTFKVVPPGVGIVHQVNLEYLARGVHKKAEGADTVYYPDSLVGTDSHT 215

Query: 208 PHVDALGVIAIGVGGLEAESVMLGRASYMRLPDIIGVELTGKPQPGITATDIVLALTEFL 267
             ++ +GV+  GVGG+EAE+ MLG+  Y   PD++GVEL GK + G+TATD+VL +TE L
Sbjct: 216 TMINGIGVVGWGVGGIEAEAGMLGQPVYFLTPDVVGVELKGKLREGLTATDLVLTVTELL 275

Query: 268 RAQKVVSSYLEFFGEGAEALTLGDRATISNMTPEFGATAAMFYIDQQTLDYLTLTGREAE 327
           R +KVV  ++EFFGEG ++L+L DRATI NM PE+GAT   F +D++T++Y   TGR   
Sbjct: 276 RKEKVVGKFVEFFGEGTKSLSLPDRATIGNMAPEYGATMGFFPVDEKTIEYFKGTGRTDA 335

Query: 328 QVKLVETYAKTAGLWS-DDLKQAVYPRTLHFDLSSVVRTIAGPSNPHARV---------- 376
           ++   E Y K  GL+      Q  Y + +  DL +V  ++AGP  P  R+          
Sbjct: 336 EISAFENYFKAQGLFGIPKAGQIDYTKVVTLDLGTVTPSLAGPKRPQDRIEIGHVKSTFS 395

Query: 377 -----PTSELA----ARGISGEVENEPGL-MPDGAVIIAAITSCTNTSNPRNVIAAGLLA 426
                P +E      A  +  +     G+ + +G ++IAAITSCTNTSNP  ++AAGLLA
Sbjct: 396 DLFSKPVAENGFAKKAADLEAQYTTSNGVDVKNGDILIAAITSCTNTSNPSVLLAAGLLA 455

Query: 427 RNANAKGLTRKPWVKTSLAPGSKAVQLYLEEANLLPELESLGFGIVGFACTTCNGMSGAL 486
           + A   GLT  P +KTSLAPGS+ V  YL + +L+  L+ LGF +  + CTTC G +G L
Sbjct: 456 KKAVEAGLTVAPHIKTSLAPGSRIVTEYLTKTDLMKYLDKLGFTLAAYGCTTCIGNAGDL 515

Query: 487 DPVIQQEVIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTIRFDIEKD 546
            P + + +   D+ A AVLSGNRNF+ RIHP  +  FLASPPLVVAYAIAG I  D+  +
Sbjct: 516 TPELNEAITKNDIVAAAVLSGNRNFEARIHPNIRANFLASPPLVVAYAIAGNITRDLMTE 575

Query: 547 VLGLDKDGKPVRLINIWPSDAEIDAVIAASVKPEQFRKVYEPMF---DLSVDYGDKVSPL 603
            +G  K GK + L +IWP+  E++ ++  ++  + FRK Y  +    DL      +   +
Sbjct: 576 PVGKGKGGKDIYLGDIWPTSEEVNELLKFALDADAFRKNYSALTKKGDLWSKIEGEEGQV 635

Query: 604 YDWRPQSTYIRRPPYWEGALAGE-----RTLKGMRPLAVLGDNITTDHLSPSNAIMMDSA 658
           YDW P+STYI  PP++    + +       +K  R L + GD++TTDH+SP+ +I  DS 
Sbjct: 636 YDW-PKSTYIAEPPFFGKDFSMQPADSIAAVKDARALGIFGDSVTTDHISPAGSIKEDSP 694

Query: 659 AGEYLHKMGLPEEDFNSYATHRGDHLTAQRATFANPKLKNEM--AIVDGKVKQGSLARIE 716
           AG++L + G+ + DFNSY + RG+H    R TFAN ++KN M  A  DG   +G L   +
Sbjct: 695 AGKWLKENGVQKADFNSYGSRRGNHDVMMRGTFANVRIKNLMIPAKADGTRVEGGLTIHQ 754

Query: 717 PEGIVTRMWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEAIVAEGFERIH 776
           P G    +++A   Y+D   P ++ AG +YG GSSRDWAAKG +L GV+ +VA  FERIH
Sbjct: 755 PSGEQLSIYDAAMKYIDAGTPTVVFAGEEYGTGSSRDWAAKGTQLLGVKVVVARSFERIH 814

Query: 777 RTNLVGMGVLPLEFKAGENRATYGIDGTEVFDVIG---SIAPRADLTVIITRKNGERVEV 833
           R+NLVGMGVLPL+FK  ++  + GI G E +D+ G      P+ ++T++I  K G+   V
Sbjct: 815 RSNLVGMGVLPLQFKGSDSVQSLGITGEETYDIEGLGADFKPQQEVTLVIRDKEGKEKRV 874

Query: 834 PVTCRLDTAEEVSIYEAGGVL 854
            V  R+DT  EV  Y+ GG+L
Sbjct: 875 QVLLRIDTPIEVDYYKHGGIL 895


Lambda     K      H
   0.318    0.136    0.397 

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: 1919
Number of extensions: 105
Number of successful extensions: 9
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: 867
Length of database: 905
Length adjustment: 43
Effective length of query: 824
Effective length of database: 862
Effective search space:   710288
Effective search space used:   710288
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