Align L-lactate dehydrogenase (cytochrome) (EC 1.1.2.3) (characterized)
to candidate BPHYT_RS31690 BPHYT_RS31690 hypothetical protein
Query= reanno::Smeli:SM_b20850 (378 letters) >FitnessBrowser__BFirm:BPHYT_RS31690 Length = 383 Score = 216 bits (549), Expect = 1e-60 Identities = 125/372 (33%), Positives = 198/372 (53%), Gaps = 4/372 (1%) Query: 7 IRDLKALARRRVPKLFFDYADSGAWTEGTYRANEEDFAG-IKLRQRVLVDMSDRSLETTM 65 +RD AR+ +P F+ GA + NE F + +R +D++ T+ Sbjct: 1 MRDFVEPARKHLPAFAFNTLAGGAGNDAGVAENEAAFGRRFFVSRRFAPASTDQT--ATV 58 Query: 66 IGQKVSMPVALAPTGLTGMQHADGEMLAAQAAEAFGVPFTLSTMSICSIEDVASVTTKPF 125 G + P +AP GL + + ++L AQAA+A PF LST + SIE + V Sbjct: 59 FGHSYASPFGVAPMGLANLFYPGADLLLAQAAQAGNFPFVLSTAASTSIERITKVAPDVS 118 Query: 126 WFQLYVMREREFVLDLIDRAKAAKCSALVMTLDLQILGQRHKDLRNGLSAPPRLTPKHLW 185 W+QLY++ + +L+ R + LV+T+D+ + G+R+ +R+G++ P R T L Sbjct: 119 WYQLYLLSDDRLNAELLSRVAGCGVAVLVLTVDVPVAGRRNSAIRDGVTLPLRWTSALLA 178 Query: 186 MMATRPGWCMKMLGTNRRTFRNIVGHAKSVADLSSLQAWTNEQFDPQLSWKDVEWIKERW 245 + RP W + ML N HA AD+ + L W D++ ++ W Sbjct: 179 DVMRRPQWALGMLRHGAPKLENYAPHA-GTADVGAASRHIASVMKMGLEWDDLKKVRAMW 237 Query: 246 GGPLILKGILDPEDAKMAAKTGADAIIVSNHGGRQLDGAHSSISMLPRIVEAVGDQIEVH 305 G L++KGIL P+DA + GAD I VSNHGGRQL+GA +S+ L I AVG V Sbjct: 238 PGKLVIKGILHPDDAARSVALGADGIWVSNHGGRQLEGAIASLDALSEIRRAVGRDTAVF 297 Query: 306 LDGGIRSGQDVLKAIALGAKGTYIGRPFLYGLGALGKEGVTLALDIIRKEMDTTMALCGK 365 LDGG+R+G+D+LKA ALGA + GR F + + A G+ GV A++I+++E+ +A G Sbjct: 298 LDGGVRTGEDILKACALGAGLCFSGRSFAFPVAAYGERGVRAAVEILKEEIRVGLAQLGV 357 Query: 366 RRITEVGRDIIA 377 + ++ + D ++ Sbjct: 358 QSLSALTSDSLS 369 Lambda K H 0.321 0.136 0.406 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: 334 Number of extensions: 17 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: 378 Length of database: 383 Length adjustment: 30 Effective length of query: 348 Effective length of database: 353 Effective search space: 122844 Effective search space used: 122844 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 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