Align alpha-ketoglutarate TRAP transporter, large permease component (characterized)
to candidate WP_092350793.1 BLU87_RS16285 TRAP transporter large permease
Query= reanno::SB2B:6938090 (466 letters) >NCBI__GCF_900107645.1:WP_092350793.1 Length = 428 Score = 265 bits (678), Expect = 2e-75 Identities = 150/455 (32%), Positives = 247/455 (54%), Gaps = 40/455 (8%) Query: 10 LFLCMLLG-----MPIAIALGFSSMLTILLFSNDSLASVALKLYEATSEHYTLLAIPFFI 64 L L +LLG +P+ +AL F+ ++ V LY + + + L+ + FF+ Sbjct: 7 LILAILLGSLAATVPVFMALFFTGTFGLVYLLGIDPQIVIEVLYRSMDK-FALVVVMFFV 65 Query: 65 LSSAFLSTGGVARRIIDFAMDSVGHIRGGLAMASVMACMLFAAVSGSSPATVAAIGSIVI 124 L ++TG + ++I A VG + GGLAMA ++AC F A+SGS+ ATV AIG +I Sbjct: 66 LCGNIMTTGSIVEKLIKTANVLVGFLPGGLAMAGILACGFFGAISGSTVATVVAIGGFMI 125 Query: 125 VGMVRAGYPQKFAAGVITTSGTLGILIPPSIVMLVYAAATEVSAARMFMAGLIPGLLMGV 184 +V Y +KF+ GV+TT+ LG++IPPSI M++YA + +F+ G +PGL++ Sbjct: 126 PALVENDYDEKFSVGVMTTAPILGVVIPPSIAMILYAMVSNDPLEELFLTGFVPGLMIMG 185 Query: 185 LLMVAIYIVARIKNLPSRPFPGVKALSLSSAKAMGGLALIFIVLGSIYGGVASPTEAAAV 244 + + Y+V + K L + P +K +++ L L ++ G IY G+ + EAA V Sbjct: 186 AMSLYAYLVCKKKGLKTIHRPNLKEALPVIRESIWALFLPVLIFGGIYSGMFTANEAAVV 245 Query: 245 ACVYAYLVAVFGYRDIGPLKEVPWRKEGEAILAAIVRNLLHVGLGLIKTPTDKEIRNVVR 304 AC YA+ V +F +RD+ L +++ V+ Sbjct: 246 ACFYAFFVEIFIHRDMKLL----------------------------------DVKRVIV 271 Query: 305 DGAKVSIMLLFIIANAMLFAHVLTTERIPHIIAETIVGWGLPPWGFLIIVNLLLLAAGNF 364 A S LL I+A A +F LT E+IP+ IA +V PW FL+ VN+LLL G F Sbjct: 272 SSAVTSATLLIIVAGASVFGEYLTFEQIPNKIATAVVSSISSPWVFLLAVNILLLIIGMF 331 Query: 365 MEPSAILLIMAPILFPIAVQLGIDPIHLGIIMVVNMEIGMLTPPVGLNLFVTAGITGRSI 424 M+ + LI+ PI P+ + GI+ +H G++M +N+ IG TPP+G++L+++ R + Sbjct: 332 MDIISATLILTPIFLPLLNKFGINTMHFGLLMTINLGIGYCTPPLGVSLYISGATVNRDL 391 Query: 425 GWVIHACLPWLLLLLGFLVLITYVPQISLFLPEYL 459 +V A +P+LL+ + L+++T+ P + LFLP ++ Sbjct: 392 VYVSKAVMPFLLIQIAILLILTFFPDLVLFLPRWV 426 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: 522 Number of extensions: 20 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 466 Length of database: 428 Length adjustment: 33 Effective length of query: 433 Effective length of database: 395 Effective search space: 171035 Effective search space used: 171035 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 24 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