Align TRAP-type large permease component (characterized, see rationale)
to candidate WP_092483295.1 BM299_RS09255 TRAP transporter large permease
Query= uniprot:Q930R2 (425 letters) >NCBI__GCF_900115975.1:WP_092483295.1 Length = 429 Score = 325 bits (834), Expect = 1e-93 Identities = 169/413 (40%), Positives = 252/413 (61%) Query: 4 VVFIVSLLGAMAIGVPVAFSLMFCGVVLMWYMGMFNTQIIAQNMIAGADTFTLLAIPFFI 63 ++ ++ LL + +G P+AFSL V + G ++ Q + D+F LLA+PFF+ Sbjct: 5 LILLLVLLLLLLVGFPIAFSLAMAAVAALLSKGTIPLTVVPQRLFTATDSFILLAVPFFV 64 Query: 64 LAGELMNAGGLSRRIIDFAIACVGHIRGGLGIVAIMAAVIMASISGSAAADTAALAAILI 123 LAGELM GG+SRR+++FA +G I GGL +V+I +A A+ISGS+AA TAA+ ++ Sbjct: 65 LAGELMQHGGISRRLVNFASDLLGWISGGLALVSIASAAFFAAISGSSAATTAAIGGVMY 124 Query: 124 PMMAKAGYNVPRSAGLIAAGGVIAPVIPPSMAFIVFGVAANVSITQLFMAGIVPGLIMGI 183 P M + GY +A + A GG + VIPPS+ I++GV SI LF+AGI+PGL+ Sbjct: 125 PEMRQRGYKPDFTAVVQAVGGTLGVVIPPSIPLIIYGVITGASIGDLFLAGIIPGLLGAA 184 Query: 184 ALVATWLLVVRKDDIQPLPRTPMKERVGATGRALWALGMPVIILGGIKAGVVTPTEAAVV 243 +A + K + + R+ +K+ + A W L MPVIILGGI GV TPTEAAVV Sbjct: 185 VYMAVAWKMAGKLGYKTMQRSSLKKTWHSFREASWGLLMPVIILGGIYGGVFTPTEAAVV 244 Query: 244 AAVYALFVGMVIYRELKPRDLPGVILQAAKTTAVIMFLVCAALVSSWLITAANIPSEITG 303 A VYAL VG IY+EL ++ +++++ T+A+IM L+ A + +W++T NIP ITG Sbjct: 245 AVVYALLVGFFIYKELNWKNFYSMLVKSGLTSAMIMLLIATASLFTWIMTIENIPQAITG 304 Query: 304 FISPLIDRPTLLMFVIMLVVLVVGTALDLTPTILILTPVLMPIIKQAGIDPVYFGVLFIM 363 I + + + + ++ +V L+ G LD IL+L P+ PI Q G+DPV+FGV+ + Sbjct: 305 AILSMTESKLVFLLLVNMVFLIAGMFLDTVAIILLLIPIFFPIALQLGVDPVHFGVIAVF 364 Query: 364 NTCIGLLTPPVGVVLNVVSGVGRVPLGKVIVGVTPFLVAQILVLFLLVLFPDI 416 N +G +TPP GV L V SGV V L K+ V P+L+A +++ LL P + Sbjct: 365 NLAVGQMTPPFGVCLFVSSGVSGVSLEKLFKAVLPYLLAAFILILLLTYVPSL 417 Lambda K H 0.331 0.145 0.430 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: 471 Number of extensions: 17 Number of successful extensions: 1 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 425 Length of database: 429 Length adjustment: 32 Effective length of query: 393 Effective length of database: 397 Effective search space: 156021 Effective search space used: 156021 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.9 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