Align alpha-ketoglutarate TRAP transporter, large permease component (characterized)
to candidate 1937061 b3578 predicted transporter (NCBI)
Query= reanno::SB2B:6938090 (466 letters) >FitnessBrowser__Keio:1937061 Length = 425 Score = 230 bits (586), Expect = 8e-65 Identities = 134/444 (30%), Positives = 239/444 (53%), Gaps = 42/444 (9%) Query: 16 LGMPIAIAL---GFSSMLTILLFSNDSLASVALKLYEATSEHYTLLAIPFFILSSAFLST 72 +G+PIA AL G + M + +F +A + ++ ++LLAIPFF+L+ ++ Sbjct: 16 IGLPIAWALLLCGAALMFWLDMFDVQIMAQTLVN----GADSFSLLAIPFFVLAGEIMNA 71 Query: 73 GGVARRIIDFAMDSVGHIRGGLAMASVMACMLFAAVSGSSPATVAAIGSIVIVGMVRAGY 132 GG+++RI+D M VGH GGL V+A M+ A++SGS+ A AA+ ++++ M A Y Sbjct: 72 GGLSKRIVDLPMKLVGHKPGGLGYVGVLAAMIMASLSGSAVADTAAVAALLVPMMRSANY 131 Query: 133 PQKFAAGVITTSGTLGILIPPSIVMLVYAAATEVSAARMFMAGLIPGLLMGVLLMVAIYI 192 P AAG+I + G + +IPPSI +++ ++ +S +++FMAG+ PG++MG LM+ + Sbjct: 132 PVNRAAGLIASGGIIAPIIPPSIPFIIFGVSSGLSISKLFMAGIAPGMMMGATLMLTWWW 191 Query: 193 VARIKNLPSRPFPGVKALSLSSAKAMGGLALIFIVLGSIYGGVASPTEAAAVACVYAYLV 252 A NLP + ++ + S + L L I++G G+ +PTEA AVA YA V Sbjct: 192 QASRLNLPRQQKATMQEIWHSFVSGIWALFLPVIIIGGFRSGLFTPTEAGAVAAFYALFV 251 Query: 253 AVFGYRDIGPLKEVPWRKEGEAILAAIVRNLLHVGLGLIKTPTDKEIRNVVRDGAKVSIM 312 A YR++ L HV +G AK + + Sbjct: 252 ATVIYREM------------------TFATLWHVLIG----------------AAKTTSV 277 Query: 313 LLFIIANAMLFAHVLTTERIPHIIAETIVGWGLPPWGFLIIVNLLLLAAGNFMEPSAILL 372 ++F++A+A + A ++T +P ++++ + P I++ + +L G M+ + +L Sbjct: 278 VMFLVASAQVSAWLITIAELPMMVSDLLQPLVDSPRLLFIVIMVAILIVGMVMDLTPTVL 337 Query: 373 IMAPILFPIAVQLGIDPIHLGIIMVVNMEIGMLTPPVGLNLFVTAGITGRSIGWVIHACL 432 I+ P+L P+ + GIDPI+ G++ ++N IG++TPP+G L V +G+ + Sbjct: 338 ILTPVLMPLVKEAGIDPIYFGVMFIINCSIGLITPPIGNVLNVISGVAKLKFDDAVRGVF 397 Query: 433 PWLLLLLGFLVLITYVPQISLFLP 456 P++L+L LV+ ++P + + LP Sbjct: 398 PYVLVLYSLLVVFVFIPDL-IILP 420 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: 516 Number of extensions: 18 Number of successful extensions: 2 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: 425 Length adjustment: 32 Effective length of query: 434 Effective length of database: 393 Effective search space: 170562 Effective search space used: 170562 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