GapMind for catabolism of small carbon sources

 

Alignments for a candidate for prpC in Burkholderia phytofirmans PsJN

Align 2-methylcitrate synthase (EC 2.3.3.5) (characterized)
to candidate BPHYT_RS27440 BPHYT_RS27440 type II citrate synthase

Query= BRENDA::Q9I5E3
         (375 letters)



>FitnessBrowser__BFirm:BPHYT_RS27440
          Length = 432

 Score =  193 bits (491), Expect = 7e-54
 Identities = 122/385 (31%), Positives = 200/385 (51%), Gaps = 21/385 (5%)

Query: 11  GLRGQVAGQTALSTVGQEGAGLTYRGYDVRDLAAAAIFEEVAYLLLYGELPNKQQLDAYL 70
           G     A  + ++ +  +   L YRGY + +LA  A F E  YLLL GELPN QQ + ++
Sbjct: 49  GFMSTAACNSEITYIDGDKGELLYRGYPIDNLAQNADFLETCYLLLKGELPNAQQKEEFV 108

Query: 71  KKLQGQRDLPQALKEVLERIPKDAHPMDVMRTGASVLGTL---EPELSFDQQRDV-ADRL 126
           K +     +   +        +DAHPM ++      L        ++     RD+ A R+
Sbjct: 109 KTVTQHTMVHDQMHFFFRGFRRDAHPMAILVAAVGALSAFYHDSLDIGNPLHRDISAIRM 168

Query: 127 LAAFPAIMTYWYRFTHEGQRIDCNSDEPTIGGHFLALLHGK-----KPSELHVKVMNVSL 181
           +A  P ++   Y++T  GQ      ++ +   +F+ ++        K +++ V+ ++  L
Sbjct: 169 IAKLPTLVAMAYKYT-VGQPFVYPKNDLSYSANFMRMMFSSPAQEYKVNDVLVRALDRIL 227

Query: 182 ILYAEHEFNASTFTARVCASTLSDLYSCVTGAIGSLRGPLHGGANEAAMELIERFSSPQE 241
           IL+A+HE NAST T R+  S+ ++ ++C+   I  L GP HGGANEAA+ ++E   S   
Sbjct: 228 ILHADHEQNASTSTVRLAGSSGANPFACIAAGIACLWGPAHGGANEAALNMLEEIGSVDN 287

Query: 242 ATAELLKMLERKD--KIMGFGHAIYKDSDPRNEVIKGWSKQLADEVG--DKVLFAVSEAI 297
               + K+ ++    K+MGFGH +YK+ DPR ++++    ++ +E+G  D  LF ++ A+
Sbjct: 288 IPEFIAKVKDKDSGVKLMGFGHRVYKNYDPRAKLMRETCHEVLEELGLHDDPLFKLAMAL 347

Query: 298 DKTMWE-----QKKLFPNADFYHASAYHFMGIPTKLFTPIFVCSRTSGWTAHVFEQRAN- 351
           +K   E      +KL+PN DFY       +GIPT +FT IF  +RT GW A   E  A+ 
Sbjct: 348 EKIALEDEYFVSRKLYPNVDFYSGIVQRALGIPTAMFTCIFAMARTVGWIAQWNEMIADP 407

Query: 352 -NRIIRPSAEYTGVEQRAFVPLEQR 375
             +I RP   + G  QR   PL +R
Sbjct: 408 EQKIGRPRQLFVGESQREATPLAKR 432


Lambda     K      H
   0.319    0.134    0.396 

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: 403
Number of extensions: 25
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: 375
Length of database: 432
Length adjustment: 31
Effective length of query: 344
Effective length of database: 401
Effective search space:   137944
Effective search space used:   137944
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 50 (23.9 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