GapMind for catabolism of small carbon sources

 

Alignments for a candidate for deh in Cupriavidus basilensis 4G11

Align Acetate/haloacid transporter, Dehp2, with a possible atypical topology (characterized)
to candidate RR42_RS24545 RR42_RS24545 hypothetical protein

Query= TCDB::F8SVK1
         (552 letters)



>FitnessBrowser__Cup4G11:RR42_RS24545
          Length = 546

 Score =  489 bits (1260), Expect = e-143
 Identities = 254/547 (46%), Positives = 352/547 (64%), Gaps = 7/547 (1%)

Query: 8   ISHAP-MTKEEKRVIFASSLGTVFEWYDFYLAGSLAAFISKSFFSGVNPTAAFIFTLLGF 66
           ++H P  T    R I+A+S+GT+FEWY+F L G+LA+ ++  FF+GV+P+ AFIF LL F
Sbjct: 1   MAHGPDATSPMSRAIWAASIGTIFEWYEFALYGALASVLADKFFAGVDPSTAFIFALLTF 60

Query: 67  AAGFAVRPFGALVFGRLGDMVGRKYTFLITIVIMGLSTCVVGFLPGYAAIGMASPVIFIA 126
           A GF +RP GALVFGR+GDM+GRK TF+ITI +MG +T  VG LP YA+ G+ SP+  + 
Sbjct: 61  AVGFMMRPLGALVFGRIGDMIGRKRTFMITICMMGGATIGVGCLPTYASAGIVSPIALLC 120

Query: 127 MRLLQGLALGGEYGGAATYVAEHAPANRRGFYTAWIQTTATLGLFLSLLVILGVRTAMGE 186
           +R+LQG + GGEY GA TYVAE++P  RRG   +W   ++T+GL LS LVIL  RT  G 
Sbjct: 121 LRILQGFSAGGEYTGALTYVAEYSPGRRRGLNMSWTTASSTVGLLLSFLVILASRTIAG- 179

Query: 187 DAFGAWGWRIPFVASLVLLGISVWIRMQLHESPAFERIKAEGKTSKAPLSEAFGQWKNLK 246
           D+F  WGWR+PF+A+ V+L +S+ +R+++ ESPAF ++++  K SKAPL +A     NL 
Sbjct: 180 DSFDDWGWRLPFLAASVMLLVSLLLRVRMDESPAFRKLRSANKLSKAPLRDALLDRANLG 239

Query: 247 IVILALIGVTAGQAVVWYTGQFYALFFLTQTLKVDGASANILIAIALLIGTPFFLFFGSL 306
            +++A   + AG   ++Y    Y  FFLT++LKVD  + N ++ +A  +  P F   G  
Sbjct: 240 RIVIA-FALCAGMTSMYYMAALYPTFFLTKSLKVDPTTVNTVVLLATALCVPVFPLAGWA 298

Query: 307 SDRIGRKPIILAGCLIAALTYFPLFKALTHYANPALEAATQKSPIVVIANPDECSFQFNP 366
            DR GRKP++L G L +AL  FP+FK L  YAN AL AA  K+PI +  +   CS  FNP
Sbjct: 299 CDRFGRKPVLLVGFLTSALLAFPVFKGLVIYANHALAAAQAKAPISIEVDRAACSLMFNP 358

Query: 367 VGTSKFTSSCDIAKSALSKAGLNYDNVAAPAGTLAQIKVGDTTIDTYD--GKAAD-AKDA 423
           +G  KF SSCD+ K AL+ AG +Y  + A  GT A+I++GD  +D YD  G +AD AK  
Sbjct: 359 LGNRKFASSCDLVKQALANAGASYQIIDAAPGTTARIRIGDDVLDAYDAGGMSADQAKAQ 418

Query: 424 GKAFDKNLGTALKAASYPPKADPSQLNWPMTVVILTILVIYVTMVYGPIAAMLVEMFPTR 483
                + L  AL+  SYP K+DP   N  + +++L +      +    I   LVEMFPTR
Sbjct: 419 SSQLSQALHAALEKYSYPGKSDPKAFNVTVVLLLLALFFASSILTVMTIGPALVEMFPTR 478

Query: 484 IRYTSMSLPYHIGNGWFGGFLPATAFAIVAAKGNIYSGLWYPIIIALATFVIGLLFVRET 543
           IRYTSM +PY++  GW GG LP   FAI A  GN   GLWYP+   + + ++ L F RET
Sbjct: 479 IRYTSMGVPYNLATGWVGGLLPTFVFAIAAQTGNSLCGLWYPVGWTILS-LVALCFFRET 537

Query: 544 KDSNIYA 550
           +D +I A
Sbjct: 538 RDIDIAA 544


Lambda     K      H
   0.325    0.139    0.422 

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: 730
Number of extensions: 34
Number of successful extensions: 5
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: 552
Length of database: 546
Length adjustment: 36
Effective length of query: 516
Effective length of database: 510
Effective search space:   263160
Effective search space used:   263160
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: 53 (25.0 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