Align L-dehydroascorbate transporter large permease subunit (characterized, see rationale)
to candidate AZOBR_RS27150 AZOBR_RS27150 membrane protein
Query= uniprot:A0A165IWV9 (425 letters) >FitnessBrowser__azobra:AZOBR_RS27150 Length = 433 Score = 253 bits (645), Expect = 1e-71 Identities = 138/372 (37%), Positives = 231/372 (62%), Gaps = 5/372 (1%) Query: 44 AQNLVAGVDSFPLLAVPFFILAGELMNSGGISRRIIDMAQAWVGHIRGGLGYVAIGAAVL 103 AQ + G+DSF LLA+PFF +AG +MN GGI+RR+ID A+ +VG + G L + I A ++ Sbjct: 49 AQRIATGLDSFALLAIPFFFMAGSIMNRGGIARRLIDCAKVFVGWMPGPLAQITILANMM 108 Query: 104 MASMSGSALADTAALATILLPMMRQQGYPMNTSAGLIASGGIIAPIIPPSMPFVIYG-VT 162 +SGSA+A +A+ + P M + GY + +A + S I +IPPS F++Y V+ Sbjct: 109 FGCVSGSAVAAASAIGGTMQPSMDKAGYDRSYTAAVNISSCITGLLIPPSGAFIVYSLVS 168 Query: 163 TNTSISALFVSGIVPGLMMGVGLIFAWRWVLRDLDLPQGEPLP-VKDRLRATARAFWAML 221 TSI+ALFV+G +PG+++G+ ++ W++ P P + RA A ++ Sbjct: 169 GGTSIAALFVAGYLPGILLGLAVMIP-AWMMAKKRGYARLPSPTLSQSSRALLSALPSLG 227 Query: 222 MPLIIIGGMKTGVFTPTEAAVVAAFYALVVALFIHREMKLADIYGVLVRAAKTTSIVMFL 281 + +++IGG+ GVFT TE + +A YAL +AL +RE+ L DI +LV T++V + Sbjct: 228 LIVVVIGGIVGGVFTATEGSAIAVVYALALAL-AYRELSLDDIGQILVDTIVATAVVALM 286 Query: 282 CAGAQVASYMITLADLPNVLTSWLGPLVENPRLLMAVMMIVLVLIGTALDLTPTILIFAP 341 + +Y+++LA++P ++ W+ + N + + ++ IVL+L+GT LD+TP ILIF P Sbjct: 287 VGTSMAMAYVMSLAEIPQIIGDWVQSVSGNWIIALLLVNIVLLLMGTFLDITPGILIFTP 346 Query: 342 VMLPIAVKAGIDPVYFGLMFVLNGAIGLITPPVGTVLNVVAGVGRISMHSVIKGVNPFLF 401 + LP+ V+ G+DPV+FG++ V N ++G+++PP G+ L + V R+S+ VI+ + P LF Sbjct: 347 IFLPVLVELGVDPVHFGVILVFNLSLGIVSPPTGSALFIGCAVARVSIEQVIRPLIP-LF 405 Query: 402 TYVLILALLVVF 413 + L+V + Sbjct: 406 AWSTAALLVVTY 417 Lambda K H 0.329 0.143 0.431 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: 503 Number of extensions: 24 Number of successful extensions: 5 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: 433 Length adjustment: 32 Effective length of query: 393 Effective length of database: 401 Effective search space: 157593 Effective search space used: 157593 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 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