Align dicarboxylate TRAP transporter (succinate, fumarate, L-malate, and alpha-ketoglutarate), large permease component (characterized)
to candidate WP_086511775.1 BZY95_RS20675 TRAP transporter large permease
Query= reanno::PV4:5208943 (465 letters) >NCBI__GCF_002151265.1:WP_086511775.1 Length = 424 Score = 290 bits (743), Expect = 5e-83 Identities = 166/448 (37%), Positives = 264/448 (58%), Gaps = 35/448 (7%) Query: 8 ISLFLCMLLGMPIAIALGFSSMLTILLFSDDSLASVALKLYESTSEHYTLLAIPFFILSS 67 +SL + G+PIA+++ +S++ I F+ L V +++ + + L+AIPFFIL+ Sbjct: 7 LSLIILFAFGVPIAVSIMLASIIGIEFFTRLPLLLVPQQMFIGIDK-FPLMAIPFFILAG 65 Query: 68 AFLSTGGVARRIIDFAMDSVGHIRGGLAMASVMACMLFAAVSGSSPATVAAIGSIVIVGM 127 ++ GG+++R++D A VG ++GGLAM V+ CM+FAAVSGSS AT AIG+I+I M Sbjct: 66 NLMAAGGISQRLVDLAKSIVGGVQGGLAMTCVLTCMMFAAVSGSSVATTFAIGAILIPAM 125 Query: 128 VRAGYPEKFAAGVITTSGTLGILIPPSIVMLVYAAATEVSAARMFMAGLIPGLMMGLLLM 187 VR GYP+ AA + +S LG+LIPPSI ++++ +T+ S ++F+AG+ PGL++G L+ Sbjct: 126 VRHGYPKPLAASIQASSAELGVLIPPSIPLILFGVSTDTSIGQLFLAGVGPGLLIGTALI 185 Query: 188 LAIYIVARIKKLPSRPFPGFRPLAISSAKAMGGLALIVIVLGSIYGGIASPTEAAAVACV 247 L +Y+ +++ IS +A L + V+V+G IYGG+ +PTEA+AVA Sbjct: 186 LFLYLFCKVRGFGLEDHKDSTSFVISFKRAWAALLMPVVVIGGIYGGVFTPTEASAVAVF 245 Query: 248 YAYFIAVFGYRDIGPLKNVSWRDSGEPLIRAILRNLGFMVLAVFKTPADKEIRHVVRDGA 307 YA + YR++ W P++R +V T A Sbjct: 246 YALLVGGLYYRELKVAD--LW-----PILRQ----------SVISTAA------------ 276 Query: 308 KVSIMLLFIIANAMLFAHVLTTERIPHLIAETIVGMGLPVWGFLIIVNLLLLAAGNFMEP 367 ++ IIA A LF+ +++ +P IA + G+ FL+ VN+LLL G F+E Sbjct: 277 -----VMLIIAAASLFSFLISRTGLPGHIAGWVTGVFDSPMTFLLAVNVLLLIVGMFIET 331 Query: 368 SAILLIMAPILFPIATQLGIDPIHLGIIMVVNMEIGMLTPPVGLNLFVTAGITGRSMGWV 427 SA +L++APIL PIA Q G+ P+H G+IMVVN+ +GM+TPP+G+NLF + S+ + Sbjct: 332 SAAILVLAPILTPIAIQFGVHPVHFGLIMVVNLALGMITPPLGVNLFAACAVAKISIDQM 391 Query: 428 IHSCIPWLALLLFFLALITYIPQISLFL 455 + + ++ ++L L ITY+P ISL L Sbjct: 392 LPWLVRFVLVVLACLVAITYMPWISLGL 419 Lambda K H 0.330 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: 579 Number of extensions: 30 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 3 Length of query: 465 Length of database: 424 Length adjustment: 32 Effective length of query: 433 Effective length of database: 392 Effective search space: 169736 Effective search space used: 169736 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 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