Align alpha-ketoglutarate TRAP transporter, large permease component (characterized)
to candidate WP_011383251.1 AMB_RS04130 TRAP transporter large permease
Query= reanno::SB2B:6938090 (466 letters) >NCBI__GCF_000009985.1:WP_011383251.1 Length = 442 Score = 186 bits (473), Expect = 1e-51 Identities = 137/474 (28%), Positives = 226/474 (47%), Gaps = 56/474 (11%) Query: 1 MTIATLFLTLFLCMLLGMPIAIALGFSSMLT---ILLFSN----DSLASVALKLYEATSE 53 M+ TL LT F +LL + + I +G + L I L N +SL L A Sbjct: 1 MSGTTLGLTAFGILLLMLVVRIHIGIAMFLAATGIYLVLNHGELNSLLFTLNNLVYARLS 60 Query: 54 HYTLLAIPFFILSSAFLSTGGVARRIIDFAMDSVGHIRGGLAMASVMACMLFAAVSGSSP 113 +Y L IP FIL F + GG+++ + A +GH +GGLA A+ AC F A+ GSS Sbjct: 61 NYDLAVIPLFILMGQFATHGGLSKALFHAAGTLIGHFKGGLAYAATAACAAFGAICGSSL 120 Query: 114 ATVAAIGSIVIVGMVRAGYPQKFAAGVITTSGTLGILIPPSIVMLVYAAATEVSAARMFM 173 AT A +G + + + R Y + A G + GTLGILIPPS+ ++VYA T+ S ++F+ Sbjct: 121 ATAATMGQVALPELTRRNYSGRLATGTLAAGGTLGILIPPSVPLVVYAVLTQESIGKLFV 180 Query: 174 AGLIPGLLMGVLLMVAIYIVARI--KNLPSRPFPGVKALSLSSAKAMGGLALIFIVLGSI 231 A +IPG++ + M I I+ + K P+ +K + + + L + +V+ I Sbjct: 181 AAVIPGIIAALGYMAVIRIIVSLDPKAGPASERVSLKEMIKAQLGIIPVLLVFLVVIVGI 240 Query: 232 YGGVASPTEAAAVACVYAYLVAVFGYRDIGPLKEVPWRKEGEAILAAIVRNLLHVGLGLI 291 YGG A+PTEAA++ ++AV V G+ Sbjct: 241 YGGWANPTEAASIGAAACGIIAV-------------------------------VSGGM- 268 Query: 292 KTPTDKEIRNVVRDGAKVSIMLLFIIANAMLFAHVLTTERIPHIIAETIVGWGLPPWGFL 351 K+++ V A + M+ ++ A L L ++P +A + G+PP L Sbjct: 269 ---RFKDLKQSVFGTAIATAMIFMVLIGADLLNSALALTQMPAELANWVKNSGMPPVAVL 325 Query: 352 IIVNLLLLAAGNFMEPSAILLIMAPILFPIAVQLGID---------PIHLGIIMVVNMEI 402 + + + G M+ A++L+ PI +P+ LG+D I GI+ ++ +EI Sbjct: 326 FTIIAIYVLLGCVMDSLAMILLTIPIFYPVV--LGLDFYGMSVDDKSIWFGIVALMVVEI 383 Query: 403 GMLTPPVGLNLFVTAGIT-GRSIGWVIHACLPWLLLLLGFLVLITYVPQISLFL 455 G++ PPVG+NL+V I + LP+L +V++ + P ++L+L Sbjct: 384 GLVHPPVGMNLYVINKIAKDVPLKETAMGVLPFLASDFIRIVVLVFFPPMALWL 437 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: 584 Number of extensions: 34 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 1 Length of query: 466 Length of database: 442 Length adjustment: 33 Effective length of query: 433 Effective length of database: 409 Effective search space: 177097 Effective search space used: 177097 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