Align anaerobic glycerol-3-phosphate dehydrogenase subunit B (EC 1.1.5.3) (characterized)
to candidate BWI76_RS19970 BWI76_RS19970 anaerobic glycerol-3-phosphate dehydrogenase subunit B
Query= ecocyc::ANGLYC3PDEHYDROGSUBUNITB-MONOMER (419 letters) >FitnessBrowser__Koxy:BWI76_RS19970 Length = 419 Score = 545 bits (1403), Expect = e-159 Identities = 267/418 (63%), Positives = 319/418 (76%) Query: 1 MRFDTVIMGGGLAGLLCGLQLQKHGLRCAIVTRGQSALHFSSGSLDLLSHLPDGQPVTDI 60 M+FD I+GGGLAGLLCGL L + GLR I++RGQSALHFSS SLDLLS LP+G+ VTD+ Sbjct: 1 MKFDCAIIGGGLAGLLCGLALNQRGLRSVIISRGQSALHFSSASLDLLSTLPNGETVTDV 60 Query: 61 HSGLESLRQQAPAHPYSLLEPQRVLDLACQAQALIAESGAQLQGSVELAHQRVTPLGTLR 120 G+ L +Q HPY+ L +RV+ A QAQAL A+ G +QG H RVTPLGTLR Sbjct: 61 AHGIGQLARQLSEHPYARLGAERVMGYASQAQALFADCGIAMQGEASQPHLRVTPLGTLR 120 Query: 121 STWLSSPEVPVWPLPAKKICVVGISGLMDFQAHLAAASLRELGLAVETAEIELPELDVLR 180 + WLS E+ PLPA +CVVGISG DFQ HLAAASL + G+ E EI+LP LDVLR Sbjct: 121 AAWLSPQEIATAPLPANGVCVVGISGFGDFQPHLAAASLNQHGVHAEAQEIDLPLLDVLR 180 Query: 181 NNATEFRAVNIARFLDNEENWPLLLDALIPVANTCEMILMPACFGLADDKLWRWLNEKLP 240 ++ +EFRA NIAR LD+E WP LL AL P+A I+MPACFGLADD+L++WL ++LP Sbjct: 181 DSPSEFRAANIARRLDDETQWPALLAALRPLAQRHRFIIMPACFGLADDRLYQWLQQRLP 240 Query: 241 CSLMLLPTLPPSVLGIRLQNQLQRQFVRQGGVWMPGDEVKKVTCKNGVVNEIWTRNHADI 300 C L LLPTLPPSV G+RL QLQR F+R GG W+ GDEV ++ +NG+VN IWTRNH DI Sbjct: 241 CPLRLLPTLPPSVPGMRLHAQLQRHFIRGGGTWLTGDEVINISQQNGIVNAIWTRNHGDI 300 Query: 301 PLRPRFAVLASGSFFSGGLVAERNGIREPILGLDVLQTATRGEWYKGDFFAPQPWQQFGV 360 PLRPRFAVLASGSFFS GLVAER+G+REPILGLD+ QT R WY+ DFFA QPWQ+FG+ Sbjct: 301 PLRPRFAVLASGSFFSNGLVAERSGVREPILGLDLQQTLPRERWYQQDFFASQPWQRFGL 360 Query: 361 TTDETLRPSQAGQTIENLFAIGSVLGGFDPIAQGCGGGVCAVSALHAAQQIAQRAGGQ 418 TD LRP GQT+ENLFA+GS+LGGFD IA GCGGGVCAV+ALHAA+ I + AGG+ Sbjct: 361 KTDAALRPQLQGQTLENLFAVGSILGGFDAIALGCGGGVCAVTALHAARLIGELAGGE 418 Lambda K H 0.321 0.137 0.426 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: 591 Number of extensions: 16 Number of successful extensions: 1 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: 419 Length of database: 419 Length adjustment: 32 Effective length of query: 387 Effective length of database: 387 Effective search space: 149769 Effective search space used: 149769 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