GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dctA in Paraburkholderia bryophila 376MFSha3.1

Align aerobic C4-dicarboxylate transport protein (characterized)
to candidate H281DRAFT_01363 H281DRAFT_01363 aerobic C4-dicarboxylate transport protein

Query= CharProtDB::CH_014038
         (428 letters)



>FitnessBrowser__Burk376:H281DRAFT_01363
          Length = 433

 Score =  489 bits (1260), Expect = e-143
 Identities = 241/419 (57%), Positives = 320/419 (76%)

Query: 2   KTSLFKSLYFQVLTAIAIGILLGHFYPEIGEQMKPLGDGFVKLIKMIIAPVIFCTVVTGI 61
           K   +++LYF V  AI IG+LLGHF P +  +MKPLGD F+KLIKM+I P+IFCTVVTGI
Sbjct: 15  KKPFYRTLYFHVFAAIIIGVLLGHFAPSLAVKMKPLGDAFIKLIKMVIGPIIFCTVVTGI 74

Query: 62  AGMESMKAVGRTGAVALLYFEIVSTIALIIGLIIVNVVQPGAGMNVDPATLDAKAVAVYA 121
           AGM  MK VGR G  ALLYFEIVST++L+IGL+  ++  PG+G N+DPAT+D KA+A Y 
Sbjct: 75  AGMGDMKKVGRVGGKALLYFEIVSTLSLVIGLVAGHIFHPGSGFNLDPATIDTKALAGYT 134

Query: 122 DQAKDQGIVAFIMDVIPASVIGAFASGNILQVLLFAVLFGFALHRLGSKGQLIFNVIESF 181
             A  Q  V F+M +IP +V GAFASGN+LQ+LL +VLFG AL   G +G+ +  +I+ F
Sbjct: 135 TAAHQQNTVEFLMHIIPDTVTGAFASGNVLQILLISVLFGAALAATGERGRPLIAMIDYF 194

Query: 182 SQVIFGIINMIMRLAPIGAFGAMAFTIGKYGVGTLVQLGQLIICFYITCILFVVLVLGSI 241
           +   FGI+++IM++A IGAFG++AFTIG YG+G +V L +LI  FY T  +FV++VLG+I
Sbjct: 195 AHTFFGIVHIIMKVAAIGAFGSIAFTIGTYGIGAVVPLLKLIGAFYATLAVFVIVVLGAI 254

Query: 242 AKATGFSIFKFIRYIREELLIVLGTSSSESALPRMLDKMEKLGCRKSVVGLVIPTGYSFN 301
           ++  GFSIF+F+ YIREE+LIVLGTSSSE+ALP+ML+K+E+LGC KSVVGLVIP GYSFN
Sbjct: 255 SRLLGFSIFRFMSYIREEILIVLGTSSSEAALPQMLEKLERLGCSKSVVGLVIPAGYSFN 314

Query: 302 LDGTSIYLTMAAVFIAQATNSQMDIVHQITLLIVLLLSSKGAAGVTGSGFIVLAATLSAV 361
           LDGT+IYLTMA +FIAQA N ++ +  Q+TL+ V +L+SKGA+GV G+ F++L +TL   
Sbjct: 315 LDGTNIYLTMAVLFIAQAFNIELSLTQQLTLVGVAMLTSKGASGVAGAAFVMLTSTLLVF 374

Query: 362 GHLPVAGLALILGIDRFMSEARALTNLVGNGVATIVVAKWVKELDHKKLDDVLNNRAPD 420
             +PV+G+ LILGI RFM    A+ N +GNGVAT+VV+ W  ELD  KL+  ++ R  D
Sbjct: 375 PLIPVSGMVLILGIHRFMGTGLAIANTIGNGVATLVVSAWEHELDRSKLNAGMSRRRAD 433


Lambda     K      H
   0.327    0.142    0.401 

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: 600
Number of extensions: 24
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: 428
Length of database: 433
Length adjustment: 32
Effective length of query: 396
Effective length of database: 401
Effective search space:   158796
Effective search space used:   158796
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 51 (24.3 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