Align DUF5009 domain-containing protein (characterized, see rationale)
to candidate CA265_RS06730 CA265_RS06730 DUF5009 domain-containing protein
Query= uniprot:A1S448 (378 letters) >FitnessBrowser__Pedo557:CA265_RS06730 Length = 408 Score = 274 bits (700), Expect = 4e-78 Identities = 167/399 (41%), Positives = 238/399 (59%), Gaps = 36/399 (9%) Query: 10 KPRLMSLDALRGFDMFWILGGEKLFIALFA--------LTGWSFWQLADA---------- 51 K RL+SLDALRGFDMFWI+ GE +F L + + S W++A Sbjct: 16 KKRLLSLDALRGFDMFWIISGEGIFHGLASGVMKEHALIRDPSDWKIATKKSLSFFEELL 75 Query: 52 -----EMHHSEWHGFTFYDLIFPLFIFLSGVALGLSPKRLDKLAPAERNP---IYRHAVK 103 ++HHS W+GFTFYDLIFPLFIF+SGVA+ S ++ +N IY ++ Sbjct: 76 IGISNQLHHSTWNGFTFYDLIFPLFIFISGVAMPFSYEKHLSTKHDNQNSAKSIYTALIR 135 Query: 104 RLFLLLALGVLYNHGWGTGIPAHSDEVRYASVLGRIAFAWFFAALLVWHTSLRTQIATAL 163 R +L+ LG++ N G + R+ASVLGRIA + FFAAL+ + S QI Sbjct: 136 RTLILIILGMVVN---GLLKWQGYEATRFASVLGRIALSTFFAALIYLNFSRNQQIIWLA 192 Query: 164 AILFGYAAIQLWLPVPGGQAGVLTPSGSINAWVDTHFLPGITYQHRPYDPEGILSTLPAI 223 IL GY + +PVPG VLTP G++ A++D +LPG ++ YDPEG+LST+PAI Sbjct: 193 GILVGYYIFMIMIPVPGFGNAVLTPEGNLAAYIDRLWLPGKLHRS-VYDPEGLLSTIPAI 251 Query: 224 VNALMGVFVGRFIVKPDARGDWAKAGILTGAGGLSLV---LGWSLDSVLPVNKDLWTSSF 280 AL+GVF G F+ + R K IL GL L+ L W++ P+NK++WTSSF Sbjct: 252 ATALLGVFTGSFLHSKNNRFTPNKKVILLLTAGLVLIFAGLFWNI--FFPINKNMWTSSF 309 Query: 281 VLVTTGWNLLFLALFYVLVDVLGAKRLAFPFVVIGVNSIIIYL-ASSLMNWEYLSKSLFG 339 VL+T G++++ LALFY ++D+ G ++ + PF+ IG NSI+IY+ A L N+E S+ LFG Sbjct: 310 VLLTGGFSVILLALFYYIIDISGHQKWSTPFIWIGTNSILIYVCAHGLFNFESTSQFLFG 369 Query: 340 GVIHALPMPAQALAAAIGFLLVQWALLYWMYRKGIFIRI 378 G+I LP+ Q G LL+Q A+L ++Y + F++I Sbjct: 370 GIITKLPLIWQQAGLWTGVLLIQLAILKFLYDRKWFLKI 408 Lambda K H 0.328 0.143 0.466 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: 566 Number of extensions: 22 Number of successful extensions: 7 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: 378 Length of database: 408 Length adjustment: 31 Effective length of query: 347 Effective length of database: 377 Effective search space: 130819 Effective search space used: 130819 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 (21.7 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