GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dctA in Azospirillum brasilense Sp245

Align C4-dicarboxylate transport protein 2 (characterized)
to candidate AZOBR_RS21140 AZOBR_RS21140 C4-dicarboxylate ABC transporter

Query= SwissProt::Q9I4F5
         (436 letters)



>FitnessBrowser__azobra:AZOBR_RS21140
          Length = 433

 Score =  520 bits (1339), Expect = e-152
 Identities = 253/406 (62%), Positives = 322/406 (79%)

Query: 3   KQPFYKSLYVQVLVAIAIGIALGHWYPETAVAMKPFGDGFVKLIKMAIAPIIFCTVVTGI 62
           K+PFY +L VQVL AI IGI LGH+YP  AV MKP GD F+K+IKM I PI+F TVVTGI
Sbjct: 9   KKPFYTNLTVQVLTAITIGILLGHFYPALAVQMKPLGDVFIKMIKMVIGPIVFLTVVTGI 68

Query: 63  AGMQSMKSVGKTGGMALLYFEVVSTVALIIGLVVVNVVQPGAGMHVDPNTLDTSKIAAYA 122
           + +  MK VGK GG A+LYFE+V+T AL +GL+VVN+V+PG+GM++   +L    +A YA
Sbjct: 69  SSIGDMKKVGKVGGKAILYFEIVTTFALGLGLLVVNLVKPGSGMNIQAGSLKADAVAKYA 128

Query: 123 AAGEKQSTVDFLMNVIPGTVVGAFANGDILQVLFFSVLFGYALHRLGSYGKPVFEFIERV 182
              +  +T+DFL+N++P  V+GAF  GD+LQ+LFF+V+FG AL  +G  GK V +  E+V
Sbjct: 129 TEAQNHTTIDFLVNIVPDNVIGAFVKGDMLQILFFAVIFGVALSAMGQKGKVVEDMFEKV 188

Query: 183 SHVMFNIINVIMKVAPIGAFGAMAFTIGAYGVGSLVQLGQLMLCFYITCILFVLIVLGGI 242
           SH +F +I ++M+VAP+GAFGAM+FTIG YGV SL  LGQLM   YIT  LFV +VLG I
Sbjct: 189 SHALFGVIGILMRVAPLGAFGAMSFTIGKYGVSSLTSLGQLMAAVYITMALFVFVVLGSI 248

Query: 243 ARAHGFSILRFIRYIREELLIVLGTSSSESALPRMIDKMEKLGCNKSVVGLVIPTGYSFN 302
           AR + FS+L F+RYI++ELLIVLGTSSSES LPRM++KM+K GC+K VVGLVIPTGYSFN
Sbjct: 249 ARLYNFSLLTFLRYIKDELLIVLGTSSSESVLPRMMEKMQKFGCSKHVVGLVIPTGYSFN 308

Query: 303 LDGTSIYLTMAAVFIAQATDTPMDITHQITLLLVLLIASKGAAGVTGSGFIVLAATLSAV 362
           LDGTSIYL+MAA+FIAQA +  + I  Q+T+L +L++ SKGAA VTG GF+ LAATLSA 
Sbjct: 309 LDGTSIYLSMAAIFIAQAFNIDLTIWQQLTILGLLMLTSKGAAAVTGGGFVTLAATLSAT 368

Query: 363 GHLPVAGLALILGIDRFMSEARALTNLVGNGVATVVVSKWCKQLDE 408
           GHLP+ GLAL+LG+DRFMSEARA+TNL+GNGVAT+VV+K   + DE
Sbjct: 369 GHLPIEGLALLLGVDRFMSEARAITNLIGNGVATIVVAKMEGEFDE 414


Lambda     K      H
   0.325    0.140    0.406 

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: 592
Number of extensions: 28
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: 436
Length of database: 433
Length adjustment: 32
Effective length of query: 404
Effective length of database: 401
Effective search space:   162004
Effective search space used:   162004
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 51 (24.3 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