Align TRAP-type large permease component (characterized, see rationale)
to candidate AZOBR_RS26625 AZOBR_RS26625 dehydroascorbate transporter
Query= uniprot:Q930R2 (425 letters) >FitnessBrowser__azobra:AZOBR_RS26625 Length = 427 Score = 548 bits (1413), Expect = e-161 Identities = 266/423 (62%), Positives = 350/423 (82%) Query: 1 MTLVVFIVSLLGAMAIGVPVAFSLMFCGVVLMWYMGMFNTQIIAQNMIAGADTFTLLAIP 60 +T+V+F+ SLLGAMA+G+P+AF+L+ G+ LM +MGM + QI+ Q+M GA++F LLA+P Sbjct: 1 VTIVIFVGSLLGAMALGLPIAFALIVSGLALMAFMGMLDPQIVVQSMWDGANSFPLLAVP 60 Query: 61 FFILAGELMNAGGLSRRIIDFAIACVGHIRGGLGIVAIMAAVIMASISGSAAADTAALAA 120 FF+LAGE MNAGG+SRRII A+A VGH+RGGLG VA+ AA++MAS+SGSA ADTAALA+ Sbjct: 61 FFMLAGEFMNAGGMSRRIIAMAMAWVGHLRGGLGFVAVFAAILMASLSGSAVADTAALAS 120 Query: 121 ILIPMMAKAGYNVPRSAGLIAAGGVIAPVIPPSMAFIVFGVAANVSITQLFMAGIVPGLI 180 IL+PMM +AGY++ RS GLIAAGG+IAPVIPPS+ I++GVA VSIT+LF+AGIVPG++ Sbjct: 121 ILLPMMRQAGYDIHRSGGLIAAGGIIAPVIPPSIGMILYGVAGQVSITKLFLAGIVPGIM 180 Query: 181 MGIALVATWLLVVRKDDIQPLPRTPMKERVGATGRALWALGMPVIILGGIKAGVVTPTEA 240 MG+AL+ TW + R++ + P+ P++ER+ T A WA+ +PV+I+GG+K GV TPTEA Sbjct: 181 MGVALLITWWWLARREILTTPPKVPLRERLRLTADAFWAMLLPVVIIGGLKTGVFTPTEA 240 Query: 241 AVVAAVYALFVGMVIYRELKPRDLPGVILQAAKTTAVIMFLVCAALVSSWLITAANIPSE 300 AVVAAVYA+FVG+VIYREL+ DL G++L AAKTTAV+MFLV AA +S+WLITA+NIP++ Sbjct: 241 AVVAAVYAMFVGLVIYRELRIADLYGLMLSAAKTTAVVMFLVAAAGISAWLITASNIPAQ 300 Query: 301 ITGFISPLIDRPTLLMFVIMLVVLVVGTALDLTPTILILTPVLMPIIKQAGIDPVYFGVL 360 + ++P++D LLM +M++VL+VGTALD PTIL++ PVLMPIIKQAGIDPVYFGVL Sbjct: 301 LADLLAPVMDNRLLLMLALMVIVLIVGTALDFAPTILLMVPVLMPIIKQAGIDPVYFGVL 360 Query: 361 FIMNTCIGLLTPPVGVVLNVVSGVGRVPLGKVIVGVTPFLVAQILVLFLLVLFPDIVIVP 420 FIMN IGL+TPPVG VLNVV GVGR+ + ++ GV PFL+AQ VLFLLVLFP++V+ P Sbjct: 361 FIMNNAIGLITPPVGTVLNVVCGVGRMSMSNLMKGVGPFLLAQTAVLFLLVLFPELVMAP 420 Query: 421 ARW 423 W Sbjct: 421 LAW 423 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: 573 Number of extensions: 17 Number of successful extensions: 2 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: 427 Length adjustment: 32 Effective length of query: 393 Effective length of database: 395 Effective search space: 155235 Effective search space used: 155235 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 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