Align alpha-ketoglutarate TRAP transporter, large permease component (characterized)
to candidate WP_086508292.1 BZY95_RS01780 TRAP transporter large permease
Query= reanno::SB2B:6938090 (466 letters) >NCBI__GCF_002151265.1:WP_086508292.1 Length = 444 Score = 252 bits (643), Expect = 2e-71 Identities = 160/468 (34%), Positives = 247/468 (52%), Gaps = 53/468 (11%) Query: 8 LTLFLCMLLGMPIAIALGFSSMLTILLFSN-DSLASVALKLYEATSEHYTLLAIPFFILS 66 + L + M +G PIA ALG S+L ++ L ++ +E + +AIP FIL Sbjct: 12 IALIVLMAIGTPIAFALGGVSLLALMYDRGLPELIYFGETFFDRIAE-FGFVAIPMFILM 70 Query: 67 SAFLSTGGVARRIIDFAMDSVGHIRGGLAMASVMACMLFAAVSGSSPATVAAIGSIVIVG 126 A +++ R + +G + GGLA++++ AC +F+A+SGSSPAT AAIG + I Sbjct: 71 GAAVASSPTGRDLYRSLDLWMGRLPGGLAVSNIGACTIFSALSGSSPATCAAIGKMGIPE 130 Query: 127 MVRAGYPQKFAAGVITTSGTLGILIPPSIVMLVYAAATEVSAARMFMAGLIPGLLMGVLL 186 M GYP AAG I GTLGILIPPS+ M++Y +TE S R+FMAG++PGL++ L Sbjct: 131 MRTRGYPDGVAAGCIAAGGTLGILIPPSVTMIIYGISTETSIGRLFMAGVLPGLMLAGLF 190 Query: 187 MVAIYIVARIKNLPSRPFPGVKALSLSSAKA------------MGGLALIFIVLGSIYGG 234 M+ I R+ + P A + KA + L +I +L ++YGG Sbjct: 191 MIWTMIACRLAGGYANPMAQAAAQVKQNIKANVDTNLKALVRVVPFLLVIAGILFALYGG 250 Query: 235 VASPTEAAAVACVYAYLVAVFGYR--DIGPLKEVPWRKEGEAILAAIVRNLLHVGLGLIK 292 VA+P+EAA V +AV YR +GP+K Sbjct: 251 VATPSEAAGVGAFLCVALAVLIYRMWQVGPIK---------------------------- 282 Query: 293 TPTDKEIRNVVRDGAKVSIMLLFIIANAMLFAHVLTTERIPHIIAETIVGWGLPPWGFLI 352 ++RD + S+M++ +IA A +FA+ L++ I +A I + W + Sbjct: 283 --------LIMRDSLRESVMIMLVIATAEVFAYALSSMFITQTVAAAIADMEVNRWVLMG 334 Query: 353 IVNLLLLAAGNFMEPSAILLIMAPILFPIAVQLGIDPIHLGIIMVVNMEIGMLTPPVGLN 412 I+NL LL AG F+ P A++++ APIL PI + DP +I+ +N+EIG++TPPVGLN Sbjct: 335 IINLFLLVAGFFLPPVAVIVMTAPILLPIILAADFDPYWFAVILTINLEIGLITPPVGLN 394 Query: 413 LFVTAGIT-GRSIGWVIHACLPWLLLLLGFLVLITYVPQISLFLPEYL 459 LF+ GI S+ ++ LP+ L ++ +VL+ P I+L+LP + Sbjct: 395 LFIIKGIAPDISLRNILLGSLPYALCMVLGIVLLCLFPGIALWLPNLI 442 Score = 27.7 bits (60), Expect = 8e-04 Identities = 34/149 (22%), Positives = 63/149 (42%), Gaps = 15/149 (10%) Query: 113 PATVAAIGSIVIVGMVRAGYPQKFAAGVITTSGTLGILIPPSIVMLVYAAATEVSAARMF 172 P T+ + +I ++ ++ G P FA G ++ L ++ + L+Y T F Sbjct: 3 PITMGIVVAIALIVLMAIGTPIAFALGGVS---LLALMYDRGLPELIYFGETFFDRIAEF 59 Query: 173 MAGLIPGLLMGVLLMVAIYIVARIKNLPSRPFPGVKALSLSSAKAMGGLALIFIVLGSIY 232 IP M +L+ A+ ++L ++L L + GGLA+ I +I+ Sbjct: 60 GFVAIP---MFILMGAAVASSPTGRDL-------YRSLDLWMGRLPGGLAVSNIGACTIF 109 Query: 233 GGV--ASPTEAAAVACVYAYLVAVFGYRD 259 + +SP AA+ + + GY D Sbjct: 110 SALSGSSPATCAAIGKMGIPEMRTRGYPD 138 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: 631 Number of extensions: 39 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 466 Length of database: 444 Length adjustment: 33 Effective length of query: 433 Effective length of database: 411 Effective search space: 177963 Effective search space used: 177963 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