Align TRAP-type large permease component (characterized, see rationale)
to candidate WP_092484450.1 BM299_RS11930 TRAP transporter large permease
Query= uniprot:Q930R2 (425 letters) >NCBI__GCF_900115975.1:WP_092484450.1 Length = 425 Score = 328 bits (840), Expect = 3e-94 Identities = 166/416 (39%), Positives = 256/416 (61%), Gaps = 1/416 (0%) Query: 1 MTLVVFIVSLLGAMAIGVPVAFSLMFCGVVLMWYMGMFNTQIIAQNMIAGADTFTLLAIP 60 M+L++F S + IGVPVAFSL + + Y G + Q + G D+F L+AIP Sbjct: 1 MSLILF-ASFFVLVLIGVPVAFSLGLSSIAALLYQGQIPLIVSVQRLFTGTDSFPLMAIP 59 Query: 61 FFILAGELMNAGGLSRRIIDFAIACVGHIRGGLGIVAIMAAVIMASISGSAAADTAALAA 120 FF++AG LMN GG+SRR++DFA A VGH GGL V MA+++ A++SGS AA TAA+ Sbjct: 60 FFMMAGALMNTGGISRRLVDFASAVVGHKTGGLAYVTAMASMLFAAVSGSGAATTAAIGG 119 Query: 121 ILIPMMAKAGYNVPRSAGLIAAGGVIAPVIPPSMAFIVFGVAANVSITQLFMAGIVPGLI 180 ++IP + K GY ++ L A+ G + VIPPS+ F++FG + VSI +LF+AGIVPG++ Sbjct: 120 MMIPALIKKGYGKEFASALQASSGSLGVVIPPSIPFVLFGFMSGVSIAELFLAGIVPGVL 179 Query: 181 MGIALVATWLLVVRKDDIQPLPRTPMKERVGATGRALWALGMPVIILGGIKAGVVTPTEA 240 + + L+ +V+ R P KE V AL AL MP IILGGI +G TPTEA Sbjct: 180 IAVLLMVVSYFMVKNGPSTLEERVPFKEMVRRFFAALPALLMPAIILGGIFSGQFTPTEA 239 Query: 241 AVVAAVYALFVGMVIYRELKPRDLPGVILQAAKTTAVIMFLVCAALVSSWLITAANIPSE 300 AV+A VY VG+ +YREL ++ + A + AV++ L+ A SW++ + IP + Sbjct: 240 AVIAVVYGFIVGIFVYRELNLANIMEAMKDAVISNAVVLMLLAFASTFSWIMASELIPQK 299 Query: 301 ITGFISPLIDRPTLLMFVIMLVVLVVGTALDLTPTILILTPVLMPIIKQAGIDPVYFGVL 360 I +S + + + ++ + +L++GT L+ TP +++L P+L+P+ + ++ V+FGVL Sbjct: 300 IAALMSSIAPNQFIFLLLVTVFLLIIGTFLETTPALILLVPILVPVAQTFDVNLVHFGVL 359 Query: 361 FIMNTCIGLLTPPVGVVLNVVSGVGRVPLGKVIVGVTPFLVAQILVLFLLVLFPDI 416 ++N IG++TPP+G+ L V S + +VPL + + PF++ I L +L P I Sbjct: 360 MVVNLAIGMVTPPLGITLFVASNISKVPLANLFRAIVPFILCMIAALLVLTFVPQI 415 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: 484 Number of extensions: 23 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: 425 Length adjustment: 32 Effective length of query: 393 Effective length of database: 393 Effective search space: 154449 Effective search space used: 154449 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