GapMind for catabolism of small carbon sources

 

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

Align aerobic C4-dicarboxylate transport protein (characterized)
to candidate H281DRAFT_01718 H281DRAFT_01718 aerobic C4-dicarboxylate transport protein

Query= CharProtDB::CH_014038
         (428 letters)



>FitnessBrowser__Burk376:H281DRAFT_01718
          Length = 452

 Score =  478 bits (1229), Expect = e-139
 Identities = 223/407 (54%), Positives = 314/407 (77%)

Query: 9   LYFQVLTAIAIGILLGHFYPEIGEQMKPLGDGFVKLIKMIIAPVIFCTVVTGIAGMESMK 68
           LY QVL  I  GILLGHFYP++G Q+KPLGD F+KLI+M++AP+IF +VV GIA M  + 
Sbjct: 13  LYLQVLIGIIAGILLGHFYPDVGSQLKPLGDLFIKLIRMLLAPIIFASVVVGIARMNDLH 72

Query: 69  AVGRTGAVALLYFEIVSTIALIIGLIIVNVVQPGAGMNVDPATLDAKAVAVYADQAKDQG 128
             GR G  ALLYFE+ STIAL++G+++VNV +PGAGMNVDP+ +D  A++ Y   A+  G
Sbjct: 73  EAGRVGVKALLYFEVASTIALLVGMVVVNVFKPGAGMNVDPSHIDGSAISTYTTAARQHG 132

Query: 129 IVAFIMDVIPASVIGAFASGNILQVLLFAVLFGFALHRLGSKGQLIFNVIESFSQVIFGI 188
           ++ F   ++P S++GAFA+G +L ++ F++L   +L RLG +     ++++ F Q +FG+
Sbjct: 133 MLDFFTSIVPNSIVGAFANGEMLPIIFFSLLLAISLARLGPRTAPFVDMLDMFLQGMFGV 192

Query: 189 INMIMRLAPIGAFGAMAFTIGKYGVGTLVQLGQLIICFYITCILFVVLVLGSIAKATGFS 248
           + ++M +APIGAFG MAFTI KYG+GTL   GQL++C Y+T I FVV+VLG + +  G S
Sbjct: 193 VRIVMYVAPIGAFGGMAFTIAKYGIGTLASFGQLMLCLYLTSIFFVVVVLGLVMRMCGLS 252

Query: 249 IFKFIRYIREELLIVLGTSSSESALPRMLDKMEKLGCRKSVVGLVIPTGYSFNLDGTSIY 308
           +FK++RYI++E+LI LGT+S+E+ LP+ML KME++GC + VVG+V+PTGY+FN DGT+IY
Sbjct: 253 LFKYLRYIKDEILITLGTASTEAVLPQMLVKMERMGCSRPVVGMVLPTGYTFNADGTAIY 312

Query: 309 LTMAAVFIAQATNSQMDIVHQITLLIVLLLSSKGAAGVTGSGFIVLAATLSAVGHLPVAG 368
           LTMAA+FIAQA N  + I  Q+ +L VLLL+SKG+AGV G+GF+ LAATL+++  +PV G
Sbjct: 313 LTMAALFIAQAMNVHLTIWDQLLVLGVLLLTSKGSAGVAGAGFVALAATLASMHKIPVEG 372

Query: 369 LALILGIDRFMSEARALTNLVGNGVATIVVAKWVKELDHKKLDDVLN 415
           L L+LG+DRF++EARA+TNL+GNGVAT+VVA+W  +LD      VLN
Sbjct: 373 LVLLLGVDRFLNEARAVTNLIGNGVATVVVARWEGQLDMNTARAVLN 419


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: 548
Number of extensions: 21
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: 452
Length adjustment: 32
Effective length of query: 396
Effective length of database: 420
Effective search space:   166320
Effective search space used:   166320
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.

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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