GapMind for catabolism of small carbon sources

 

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

Align Organic acid uptake porter, DctA of 444 aas and 8 - 10 putative TMSs (characterized)
to candidate H281DRAFT_01363 H281DRAFT_01363 aerobic C4-dicarboxylate transport protein

Query= TCDB::Q848I3
         (444 letters)



>FitnessBrowser__Burk376:H281DRAFT_01363
          Length = 433

 Score =  479 bits (1232), Expect = e-140
 Identities = 236/414 (57%), Positives = 316/414 (76%)

Query: 4   RQPLYKSLYFQVIVAIAIGILLGHFYPQTGVALKPLGDGFIKLIKMVIAPIIFCTVVSGI 63
           ++P Y++LYF V  AI IG+LLGHF P   V +KPLGD FIKLIKMVI PIIFCTVV+GI
Sbjct: 15  KKPFYRTLYFHVFAAIIIGVLLGHFAPSLAVKMKPLGDAFIKLIKMVIGPIIFCTVVTGI 74

Query: 64  AGMQNMKSVGKTGGYALLYFEIVSTIALLIGLVVVNVVQPGNGMHIDVSTLDASKVAAYV 123
           AGM +MK VG+ GG ALLYFEIVST++L+IGLV  ++  PG+G ++D +T+D   +A Y 
Sbjct: 75  AGMGDMKKVGRVGGKALLYFEIVSTLSLVIGLVAGHIFHPGSGFNLDPATIDTKALAGYT 134

Query: 124 TAGKDQSIVGFILNVIPNTIVGAFANGDILQVLMFSVIFGFALHRLGAYGKPVLDFIDRF 183
           TA   Q+ V F++++IP+T+ GAFA+G++LQ+L+ SV+FG AL   G  G+P++  ID F
Sbjct: 135 TAAHQQNTVEFLMHIIPDTVTGAFASGNVLQILLISVLFGAALAATGERGRPLIAMIDYF 194

Query: 184 AHVMFNIINMIMKLAPIGALGAMAFTIGAYGVGSLVQLGQLMICFYITCVLFVLVVLGAI 243
           AH  F I+++IMK+A IGA G++AFTIG YG+G++V L +L+  FY T  +FV+VVLGAI
Sbjct: 195 AHTFFGIVHIIMKVAAIGAFGSIAFTIGTYGIGAVVPLLKLIGAFYATLAVFVIVVLGAI 254

Query: 244 CRAHGFSVLKLIRYIREELLIVLGTSSSESALPRMLIKMERLGAKKSVVGLVIPTGYSFN 303
            R  GFS+ + + YIREE+LIVLGTSSSE+ALP+ML K+ERLG  KSVVGLVIP GYSFN
Sbjct: 255 SRLLGFSIFRFMSYIREEILIVLGTSSSEAALPQMLEKLERLGCSKSVVGLVIPAGYSFN 314

Query: 304 LDGTSIYLTMAAVFIAQATDTHMDITHQITLLLVLLLSSKGAAGVTGSGFIVLAATLSAV 363
           LDGT+IYLTMA +FIAQA +  + +T Q+TL+ V +L+SKGA+GV G+ F++L +TL   
Sbjct: 315 LDGTNIYLTMAVLFIAQAFNIELSLTQQLTLVGVAMLTSKGASGVAGAAFVMLTSTLLVF 374

Query: 364 GHLPVAGLALILGIDRFMSEARALTNLVGNAVATVVVAKWVKELDEDQLQAELA 417
             +PV+G+ LILGI RFM    A+ N +GN VAT+VV+ W  ELD  +L A ++
Sbjct: 375 PLIPVSGMVLILGIHRFMGTGLAIANTIGNGVATLVVSAWEHELDRSKLNAGMS 428


Lambda     K      H
   0.326    0.142    0.402 

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: 623
Number of extensions: 27
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: 444
Length of database: 433
Length adjustment: 32
Effective length of query: 412
Effective length of database: 401
Effective search space:   165212
Effective search space used:   165212
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 (21.6 bits)
S2: 51 (24.3 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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