Align TRAP-type large permease component (characterized, see rationale)
to candidate SM_b20321 SM_b20321 hypothetical protein
Query= uniprot:Q930R2 (425 letters) >FitnessBrowser__Smeli:SM_b20321 Length = 421 Score = 286 bits (732), Expect = 8e-82 Identities = 157/424 (37%), Positives = 248/424 (58%), Gaps = 8/424 (1%) Query: 4 VVFIVSLLGAMAIGVPVAFSLMFCGVVLMWYMGM-FNTQIIAQNMIAGADTFTLLAIPFF 62 +V + L M +GVP+ L +V ++ G Q + G D + L++IP F Sbjct: 1 MVTTAAFLAFMLVGVPIGVCLCLGSIVYIFASGNPLLFQSFPTQLFGGVDNYGLISIPLF 60 Query: 63 ILAGELMNAGGLSRRIIDFAIACVGHIRGGLGIVAIMAAVIMASISGSAAADTAALAAIL 122 +L GE+MN GG++RRIID +A VG +RGGL V ++A + +ASI GSA A A +A ++ Sbjct: 61 VLIGEIMNGGGITRRIIDMTMAFVGAMRGGLAYVNLLANMFVASILGSATAQVAVMAQMM 120 Query: 123 IPMMAKAGYNVPRSAGLIAAGGVIAPVIPPSMAFIVFGVAANVSITQLFMAGIVPGLIMG 182 +P M K GY+ +AGL A G++ P+IPPS+ F+V+ V A V ++ + AGIVPG+++ Sbjct: 121 VPEMEKKGYDKTFAAGLTAYSGMLGPIIPPSIMFVVYSVLAQVPVSDMLAAGIVPGILLT 180 Query: 183 IALVATWLLVVRKDDIQPLP---RTPMKERVGATGRALWALGMPVIILGGIKAGVVTPTE 239 +A L++ + P R ++ERV AL L +P +I+G I +G+ TE Sbjct: 181 VAFC---LVIAAMGFVYNYPRGERMKLQERVRIVLDALPTLLIPFVIVGSILSGLANATE 237 Query: 240 AAVVAAVYALFVGMVIYRELKPRDLPGVILQAAKTTAVIMFLVCAALVSSWLITAANIPS 299 AA V AV A+ VG ELK DLP ++L+A +AV++FLV AA V SW++ +P Sbjct: 238 AAAVGAVAAVLVGCFWIGELKFSDLPRMMLRAGIYSAVVLFLVAAAAVFSWVLVYGMVPQ 297 Query: 300 EITGFISPLIDRPTLLMFVIMLVVLVVGTALDLTPTILILTPVLMPIIKQA-GIDPVYFG 358 ++ G++ + P M ++ +++LV+GT +D P +++ P+L+PI + GIDP++FG Sbjct: 298 QVAGWVQTVASDPVTFMLLVNVILLVIGTVIDGAPGLIMTVPILLPIATEVYGIDPIHFG 357 Query: 359 VLFIMNTCIGLLTPPVGVVLNVVSGVGRVPLGKVIVGVTPFLVAQILVLFLLVLFPDIVI 418 V+ ++N +G L+PPVG+ V + V GK+ + PF L+L LL L P + Sbjct: 358 VVVVVNLVLGFLSPPVGLCFFVAAAVTGAKPGKMFLVTLPFFFVSCLMLVLLSLIPSLST 417 Query: 419 VPAR 422 AR Sbjct: 418 FFAR 421 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: 490 Number of extensions: 32 Number of successful extensions: 3 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: 421 Length adjustment: 32 Effective length of query: 393 Effective length of database: 389 Effective search space: 152877 Effective search space used: 152877 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: 50 (23.9 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