Align alpha-ketoglutarate TRAP transporter, large permease component (characterized)
to candidate WP_110805808.1 C8J30_RS10490 TRAP transporter large permease subunit
Query= reanno::SB2B:6938090 (466 letters) >NCBI__GCF_003217355.1:WP_110805808.1 Length = 440 Score = 400 bits (1027), Expect = e-116 Identities = 226/473 (47%), Positives = 302/473 (63%), Gaps = 49/473 (10%) Query: 1 MTIATLFLTLFLCMLLGMPIAIALGFSSMLTILLFSNDSLASVALKLYEATSEHYTLLAI 60 M+ +F L ML GMPI+I+LG + + + + + +VALKL+ E + ++AI Sbjct: 1 MSALIIFGLLIALMLTGMPISISLGLTVLTFLFTMTEVPIDTVALKLFTGI-EKFEIMAI 59 Query: 61 PFFILSSAFLSTGGVARRIIDFAMDSVGHIRGGLAMASVMACMLFAAVSGSSPATVAAIG 120 PFFIL+ FL+ GGVA+R+I+FA VGH GGL +A V+AC LFAAVSGSSPATV AIG Sbjct: 60 PFFILAGNFLTHGGVAKRMINFATAMVGHWHGGLGLAGVIACALFAAVSGSSPATVVAIG 119 Query: 121 SIVIVGMVRAGYPQKFAAGVITTSGTLGILIPPSIVMLVYAAAT--------------EV 166 S+++ MV G+P++F AGVITTSG LGILIPPSIVM++YA AT Sbjct: 120 SVILPAMVNQGFPKQFGAGVITTSGALGILIPPSIVMVMYAVATSGMVVTGPNGEAVSSA 179 Query: 167 SAARMFMAGLIPGLLMGVLLMVAIYIVARIKNLPSRPFPGVKALSLSSAKAMGGLALIFI 226 S ++FMAG++PGL++ L + AR P + + +A GL LI + Sbjct: 180 SVGQLFMAGVVPGLMLAGFLAFTTWNRARKFGYPRLEKASLGQRFAAFREAFWGLMLIVV 239 Query: 227 VLGSIYGGVASPTEAAAVACVYAYLVAVFGYRDIGPLKEVPWRKEGEAILAAIVRNLLHV 286 V+G IY G+ +PTEAAA++ VYA++++VF Y+D+ L++VP Sbjct: 240 VIGGIYAGIFTPTEAAAMSAVYAFVISVFVYKDL-TLRDVP------------------- 279 Query: 287 GLGLIKTPTDKEIRNVVRDGAKVSIMLLFIIANAMLFAHVLTTERIPHIIAETIVGWGLP 346 V+ A +S MLL+II NA+LF+ ++ E IP + E +V GL Sbjct: 280 --------------RVLLSSANMSAMLLYIITNAVLFSFLMAHEGIPQALGEWMVNAGLS 325 Query: 347 PWGFLIIVNLLLLAAGNFMEPSAILLIMAPILFPIAVQLGIDPIHLGIIMVVNMEIGMLT 406 W FLIIVN+LLLAAGNFMEPS+I+LIMAPILFP+AV+LGIDP+H GI++VVNME+GM Sbjct: 326 WWMFLIIVNVLLLAAGNFMEPSSIVLIMAPILFPVAVRLGIDPVHFGIMIVVNMEVGMCH 385 Query: 407 PPVGLNLFVTAGITGRSIGWVIHACLPWLLLLLGFLVLITYVPQISLFLPEYL 459 PPVGLNL+V +GIT I + A PWLL +L FLVL+TYVP ISLFLP L Sbjct: 386 PPVGLNLYVASGITKMGITELTVAVWPWLLTMLVFLVLVTYVPTISLFLPHLL 438 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: 622 Number of extensions: 33 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: 440 Length adjustment: 33 Effective length of query: 433 Effective length of database: 407 Effective search space: 176231 Effective search space used: 176231 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