Align L-proline and D-alanine ABC transporter, permease component 1 (characterized)
to candidate BPHYT_RS31740 BPHYT_RS31740 ABC transporter permease
Query= reanno::azobra:AZOBR_RS08235 (301 letters) >FitnessBrowser__BFirm:BPHYT_RS31740 Length = 316 Score = 276 bits (706), Expect = 4e-79 Identities = 152/311 (48%), Positives = 214/311 (68%), Gaps = 19/311 (6%) Query: 1 MEYFLQQLINGLSLGAIYGLIAIGYTMVYGIIGMINFAHGEIYMIGAFVAL--ITFLAIG 58 M+ F+QQ+INGL LG++Y +IA+GYTMVYGI+G+INFAHG++ M+GA VAL IT L Sbjct: 1 MDIFIQQIINGLVLGSVYAIIALGYTMVYGILGIINFAHGDVLMVGAMVALSAITVLQDH 60 Query: 59 SLGITWVPLALLVMLVASMLFTAVYGWTVERIAYRPLRSSPRLAPLISAIGMSIFLQNYV 118 + VP L+ +++A+ + A+ G+T+E++AYRPLR +PRLAPLI+AIG+SI LQ Sbjct: 61 FPELGHVPTLLIALILAAAV-CAMVGYTIEKVAYRPLRRAPRLAPLITAIGVSILLQTAA 119 Query: 119 QILQGARSKPLQPILP-GNLTLMD------GAVSVSYVRLATIVITIALMYGFTQLITRT 171 I+ G +LP L L+ GAV +S +A +V+ +M G L+ RT Sbjct: 120 MIIWGRNPLAFPQLLPTAPLNLIQASENHPGAV-ISLTEIAIVVVAFFVMAGLLLLVHRT 178 Query: 172 SLGRAQRACEQDKKMAGLLGVNVDRVISLTFVMGAALAAVAGMMVLLIYGVIDFYIGFLA 231 LGRA RA ++ +A L+GVN VIS TF++G+ALAA+AG+M+ YG FY+GF+ Sbjct: 179 KLGRAMRAIAENPNVASLMGVNPGFVISATFMIGSALAALAGVMIASEYGNAHFYMGFIP 238 Query: 232 GVKAFTAAVLGGIGSLPGAMLGGVVIGLIEAFWSGYM--------GSEWKDVATFTILVL 283 G+KAFTAAVLGGIG+L GAM+GGV++GL+E +GY+ GS ++DV F +L+ Sbjct: 239 GLKAFTAAVLGGIGNLGGAMVGGVILGLVEQLGAGYIGTLTGGVFGSNYQDVFAFVVLIA 298 Query: 284 VLIFRPTGLLG 294 VL+FRP+GLLG Sbjct: 299 VLVFRPSGLLG 309 Lambda K H 0.329 0.144 0.425 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: 390 Number of extensions: 18 Number of successful extensions: 4 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: 301 Length of database: 316 Length adjustment: 27 Effective length of query: 274 Effective length of database: 289 Effective search space: 79186 Effective search space used: 79186 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: 48 (23.1 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