Align alpha-ketoglutarate TRAP transporter, large permease component (characterized)
to candidate SM_b20444 SM_b20444 hypothetical protein
Query= reanno::SB2B:6938090 (466 letters) >FitnessBrowser__Smeli:SM_b20444 Length = 468 Score = 253 bits (645), Expect = 1e-71 Identities = 156/467 (33%), Positives = 259/467 (55%), Gaps = 17/467 (3%) Query: 9 TLFLCMLLGMPIAIALGFSSMLTILLFSNDSLASVALKLYEATSEHYTLLAIPFFILSSA 68 + + ML+G+P+AI++ +S+L ++ + N + +A + A E + LLA+PFFIL+ Sbjct: 7 SFLVLMLVGVPVAISMAAASVLYLVSY-NVAPDIIAAQRMIAGVESFPLLAVPFFILAGN 65 Query: 69 FLSTGGVARRIIDFAMDSVGHIRGGLAMASVMACMLFAAVSGSSPATVAAIGSIVIVGMV 128 +++ GV RI FA+ VG ++GGLA +++ ++F+ +SG++ A A IG+I I M Sbjct: 66 LMNSAGVTGRIYSFAVALVGWMKGGLAQVNIVGSVIFSGMSGTALADAAGIGTIEIKAMK 125 Query: 129 RAGYPQKFAAGVITTSGTLGILIPPSIVMLVYAAATEVSAARMFMAGLIPGLLMGVLLMV 188 GYP A GV S TLG + PPS+ ++Y VS +FMAG++PG++M VL+M+ Sbjct: 126 DHGYPVDAAVGVTAASATLGPIFPPSLPFVIYGMMANVSIGALFMAGVVPGVVMTVLMML 185 Query: 189 AIYIVARIKNLPSRPFPGVKALSLSSAKAMGGLALIFIVLGSIYGGVASPTEAAAVACVY 248 + I A + S +K L +S + + LA+ + + G++ AV Sbjct: 186 TVAIFAYKRGWGSDTPFEMKRLLAASLEVVVVLAVPLFIYLLMAAGLSMNL---AVGIAL 242 Query: 249 AYLVAVFGYRDIGPLKEVP------------WRKEGEAILAAIVRNLLHVGLGLIKTPTD 296 L+A+ Y D + + W EA +AA++ +L +GL +T T Sbjct: 243 VVLLALDWYFDFSAVMALMTPIILIGGMTMGWFTPTEAAVAAVIWSLF-LGLVRYRTMTM 301 Query: 297 KEIRNVVRDGAKVSIMLLFIIANAMLFAHVLTTERIPHIIAETIVGWGLPPWGFLIIVNL 356 + D + + +LFI+ A +FA +LT + +++ I+ W FLI+VNL Sbjct: 302 STLARATFDTIETTASVLFIVTAASIFAWLLTVSQAAQMLSGAILTITDNKWVFLILVNL 361 Query: 357 LLLAAGNFMEPSAILLIMAPILFPIAVQLGIDPIHLGIIMVVNMEIGMLTPPVGLNLFVT 416 L+L G F++ A + I+ PIL P+ Q GIDP+H G+IM +N+ IG+L PP+G+ LFV Sbjct: 362 LMLFVGCFLDTIAAITILVPILLPLTAQFGIDPVHFGLIMTLNLMIGLLHPPLGMVLFVL 421 Query: 417 AGITGRSIGWVIHACLPWLLLLLGFLVLITYVPQISLFLPEYLDSLR 463 + + S+ A LPWL+ L L+LIT+VP + L+LP+ + +R Sbjct: 422 SRVAKLSVERTTMAILPWLVPLFIALILITFVPAVVLWLPQSVGLIR 468 Lambda K H 0.329 0.144 0.424 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: 629 Number of extensions: 37 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: 466 Length of database: 468 Length adjustment: 33 Effective length of query: 433 Effective length of database: 435 Effective search space: 188355 Effective search space used: 188355 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 (21.8 bits) S2: 51 (24.3 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