Align alpha-ketoglutarate TRAP transporter, large permease component (characterized)
to candidate WP_020922288.1 RHE_RS18500 TRAP transporter large permease subunit
Query= reanno::SB2B:6938090 (466 letters) >NCBI__GCF_000092045.1:WP_020922288.1 Length = 497 Score = 175 bits (444), Expect = 3e-48 Identities = 134/460 (29%), Positives = 214/460 (46%), Gaps = 51/460 (11%) Query: 6 LFLTLFLCMLLGMPIAIALGFSSMLTILL------FSNDSLASVALKLYEATSEHYTLLA 59 +FL + + ML G P+A +L M ++ FS L ++ L+ + S LLA Sbjct: 11 MFLGMVIFMLYGFPVAFSLAAVGMFFGIIGIVTGHFSEAFLQALPLRFFGIVSNDL-LLA 69 Query: 60 IPFFILSSAFLSTGGVARRIIDFAMDSVGHIRGGLAMASVMACMLFAAVSGSSPATVAAI 119 IPFF L A L G+A +++ G I GGLA A ++ + A++G+ A+V + Sbjct: 70 IPFFTLMGAVLERCGLAEDLLEGTGKLFGGIPGGLAYAVILVGAVLGAITGTVAASVITM 129 Query: 120 GSIVIVGMVRAGYPQKFAAGVITTSGTLGILIPPSIVMLVYAAATEVSAARMFMAGLIPG 179 G I + M+R GY + A GVI SGT+ +IPPS+V++V A S M++ + P Sbjct: 130 GVISLPIMLRYGYSPRLATGVIAASGTITQVIPPSLVLVVLADQLGRSVGDMYLGAIGPS 189 Query: 180 LLMGVL--LMVAIYIVARIKNLPSRP--FPGVKALSLSSAKAMG---GLALIFIVLGSIY 232 +L + L V + + R K++P P G +L MG + LIF+VLG+I+ Sbjct: 190 ILQVTIFVLFVLVMSIVRPKSMPPLPKEVRGDFNWALLVKVLMGMVPSIVLIFLVLGTIF 249 Query: 233 GGVASPTEAAAVACVYAYLVAVFGYRDIGPLKEVPWRKEGEAILAAIVRNLLHVGLGLIK 292 G+A+PTEA A+ V A L+A R PL Sbjct: 250 MGLATPTEAGALGVVGAMLLAAMNRRLTWPL----------------------------- 280 Query: 293 TPTDKEIRNVVRDGAKVSIMLLFIIANAMLFAHVLTTERIPHIIAETIVGWGLPPWGFLI 352 IR + ++ M++ I+ + F+ V I + G P GFLI Sbjct: 281 ------IREAMTSTTHITSMVVMILIGSTCFSLVFQGMDGSRWIEHMLSGIPGGPVGFLI 334 Query: 353 IVNLLLLAAGNFMEPSAILLIMAPILFPIAVQLGIDPIHLGIIMVVNMEIGMLTPPVGLN 412 VN+ + F++ I I+ P+L P+A LGID I G+++ VNM+ + PP G Sbjct: 335 FVNIFIFVLAFFLDFFEIAFIVIPMLAPVASSLGIDLIWFGVLICVNMQTSFMHPPFGFA 394 Query: 413 LFVTAGITGRSI--GWVIHACLPWLLLLLGFLVLITYVPQ 450 LF I + + + LPW+ + + + ++ + PQ Sbjct: 395 LFYLRSIASKDVKTSDIYMGALPWVGMQIILVAIVIFWPQ 434 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: 664 Number of extensions: 40 Number of successful extensions: 4 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: 497 Length adjustment: 34 Effective length of query: 432 Effective length of database: 463 Effective search space: 200016 Effective search space used: 200016 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: 52 (24.6 bits)
This GapMind analysis is from Apr 09 2024. 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