Align DUF1624 domain-containing protein (characterized, see rationale)
to candidate 353145 BT3619 conserved hypothetical protein (NCBI ptt file)
Query= uniprot:L0FVP4 (369 letters) >FitnessBrowser__Btheta:353145 Length = 372 Score = 224 bits (570), Expect = 4e-63 Identities = 132/373 (35%), Positives = 204/373 (54%), Gaps = 15/373 (4%) Query: 4 QRILALDVFRGITIFAMILVNNPGSWSHVYAPLLHAKWHGCTPTDLIFPFFLFIVGVAIE 63 +R+LALDV RGITI MILVN PGSW H YAPL HA+W G TPTDL+FPFF+FI+G++ Sbjct: 8 KRLLALDVMRGITIAGMILVNTPGSWQHAYAPLKHAEWIGLTPTDLVFPFFMFIMGISTY 67 Query: 64 LSLGG-QLKKGTPKGFLLRKSLIRALKLIGLGLLLTAIPYFD-----LAHLRFPGVLQRI 117 +SL P G + K + + LIG+G+ +I F + +R GV+QR+ Sbjct: 68 ISLRKYNFTFSVPAGLKILKRTV-IIFLIGIGISWLSILCFQHDPFPIDQIRILGVMQRL 126 Query: 118 GLVYFISTVMYLYWSPKALVFSSGILLIGYWLCMTFIPVPGIGPANLEPGTNLAAWIDQQ 177 L Y ++ ++ L K + + +LLI Y+ + +G + TN+ + +D+ Sbjct: 127 ALGYGVTAIVALLMKHKYIPYLIAVLLISYFAILA------LGNGYVYDETNILSIVDRA 180 Query: 178 VL-TGHMWSQTKTWDPEGLFSTLPAIVTCLLGVACGKILTGNSSHKARLTKWGIAGVTLV 236 VL H++ + DPEGL ST+ AI L+G GK+L +L + + G L Sbjct: 181 VLGQAHIYGG-QILDPEGLLSTISAIAHVLIGFCAGKLLMEVKDIHEKLERLFLIGTILT 239 Query: 237 FGGLAWSLFFPLNKALWTSSFVLYTAGWAFLGLAACYWILDVKGWKKWSLPFVIYGMNAI 296 F G S P+ K +W+ SFVL T G LA WI+D+KG+K WS F +G+N + Sbjct: 240 FAGFLLSYGSPICKKVWSPSFVLVTCGLGSSFLALLVWIIDIKGYKNWSRFFESFGVNPL 299 Query: 297 TVFFLSGVIAKLFGLIKVNWEGTRVSLKLFLQEALFNGWLAPKDASLCGAILMMIILFIP 356 ++ L+ ++A +I + ++G SL ++ AL K SL A+L +++ + Sbjct: 300 FIYVLADILAITLAVIPMTYQGEATSLHGYIYSALLQPVFGDKGGSLVFALLFVLLNWAI 359 Query: 357 AYFMWKRNIIIKV 369 Y ++K+ I IK+ Sbjct: 360 GYILYKKKIYIKI 372 Lambda K H 0.329 0.145 0.486 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: 492 Number of extensions: 29 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: 369 Length of database: 372 Length adjustment: 30 Effective length of query: 339 Effective length of database: 342 Effective search space: 115938 Effective search space used: 115938 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: 49 (23.5 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