Align alpha-ketoglutarate TRAP transporter, large permease component (characterized)
to candidate WP_092350665.1 BLU87_RS15920 TRAP transporter large permease
Query= reanno::SB2B:6938090 (466 letters) >NCBI__GCF_900107645.1:WP_092350665.1 Length = 426 Score = 264 bits (674), Expect = 5e-75 Identities = 155/452 (34%), Positives = 250/452 (55%), Gaps = 39/452 (8%) Query: 7 FLTLFLCMLLGMPIAIALGFSSMLTILLFSNDSLASVALKLYEATSEHYTLLAIPFFILS 66 F+ + L G+P+A +LG S+ L +L + +A + KL+ + + L AIP FIL+ Sbjct: 6 FVLFIVFALFGVPVAFSLGVSA-LVFMLANGIPMALIGQKLFTGM-DSFLLTAIPLFILA 63 Query: 67 SAFLSTGGVARRIIDFAMDSVGHIRGGLAMASVMACMLFAAVSGSSPATVAAIGSIVIVG 126 ++ G+ +I+F+ VG IRGGLA +V+ M+FA ++G+ + AA+GSI+I G Sbjct: 64 GNLMNAAGLTEELIEFSKLFVGRIRGGLAYTNVLISMIFAGMTGAGVSDTAAVGSIMIPG 123 Query: 127 MVRAGYPQKFAAGVITTSGTLGILIPPSIVMLVYAAATEVSAARMFMAGLIPGLLMGVLL 186 M R GY + ++ V S T+G +IPPSI +VY + T +S +F+AG+IPG+L+G Sbjct: 124 MARDGYKKDYSTAVTVISSTIGPVIPPSIPFIVYGSITGISVGALFVAGIIPGILLGASQ 183 Query: 187 MVAIYIVARIKNLP--SRPFPGVKALSLSSAKAMGGLALIFIVLGSIYGGVASPTEAAAV 244 MVAI++ +R LP + P + + ++ A+ L + I+LG I GG+A+PTE+A + Sbjct: 184 MVAIFLGSRRHKLPRIEKKIPVRQKIRITKC-AILALMMPVIILGGIIGGIATPTESAGI 242 Query: 245 ACVYAYLVAVFGYRDIGPLKEVPWRKEGEAILAAIVRNLLHVGLGLIKTPTDKEIRNVVR 304 A YA L+ VF YR I P K LIK V+ Sbjct: 243 AAFYALLIGVFVYRSITPRK-------------------------LIK---------VLI 268 Query: 305 DGAKVSIMLLFIIANAMLFAHVLTTERIPHIIAETIVGWGLPPWGFLIIVNLLLLAAGNF 364 D + ++ ++ A +F+++L E+ P ++E ++ L+++NL LL G F Sbjct: 269 DSGVTTGAVMILLGTAAIFSYLLAAEQFPQTVSEAVLSATNNKILILLLINLFLLVFGMF 328 Query: 365 MEPSAILLIMAPILFPIAVQLGIDPIHLGIIMVVNMEIGMLTPPVGLNLFVTAGITGRSI 424 ++ LLIM P+ P+A +G+DPIH G+I V+N+ IG+ TPPVG+ LFV A I I Sbjct: 329 LDVVPALLIMTPVFLPLAQHVGVDPIHYGVICVLNLAIGLATPPVGMCLFVGANIAKLPI 388 Query: 425 GWVIHACLPWLLLLLGFLVLITYVPQISLFLP 456 + +P+++ L++ TY + LFLP Sbjct: 389 EKITRPLMPFIIASFLALLVTTYWADLILFLP 420 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: 568 Number of extensions: 34 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: 2 Length of query: 466 Length of database: 426 Length adjustment: 32 Effective length of query: 434 Effective length of database: 394 Effective search space: 170996 Effective search space used: 170996 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