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.
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:
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