Align phosphopentomutase (EC 5.4.2.7) (characterized)
to candidate BPHYT_RS14155 BPHYT_RS14155 phosphoglucosamine mutase
Query= BRENDA::Q6I7B6 (450 letters) >FitnessBrowser__BFirm:BPHYT_RS14155 Length = 452 Score = 149 bits (376), Expect = 2e-40 Identities = 149/485 (30%), Positives = 227/485 (46%), Gaps = 77/485 (15%) Query: 2 RLFGTAGIRGTLWE-KVTPELAMKVGMAVGTYKSGK-----------ALVGRDGRTSSVM 49 R FGT GIRG + E +TPE +++G A G +G L+G+D R S M Sbjct: 4 RYFGTDGIRGKVGEGPITPEFVLRLGYAAGKVLAGADRWAKSGTRPTVLIGKDTRVSGYM 63 Query: 50 LKNAMISGLLSTGMEVLDADLIPTPALAWGTRKL-ADAGVMITASHNPPTDNGVKVFNGD 108 L+ A+ SG + G++V+ A +PTP +A+ TR L AGV+I+ASHNP DNG+K F+ D Sbjct: 64 LEAALESGFSAAGVDVMLAGPMPTPGIAYLTRALRLAAGVVISASHNPYYDNGIKFFSAD 123 Query: 109 GTEFYVEQERGLEEII-------FSGNFRKARWDEIKPVRNVEVIPDYINAVLDFVGHET 161 G + E E +EE + S KAR + R +E A D G Sbjct: 124 GNKLPDEVESQIEEQLDLPLACAASEQLGKARRLDDAAGRYIEFCKSTFPAAFDLHG--- 180 Query: 162 NLKVLYDGANGAGSLVAPYLLREMGAKVLSVNA-----HVDGHFPGRKPEPRYENIAYLG 216 LK++ D A+GA VAP++ E+GA+V+ + +++ P+ L Sbjct: 181 -LKLVVDCAHGAAYDVAPHVFHELGAEVIPIGVAPNGFNINDGVGATAPDA-------LV 232 Query: 217 KLVRELGVDLAIAQDGDADRIAVFDEKGNYVDEDTVIALFAKLYVEEHGG-GTVVVSIDT 275 + VR DL IA DGDADR+ V D G + D ++ + K V G V ++ T Sbjct: 233 RAVRANHADLGIALDGDADRLQVVDAAGRLYNGDELLYILVKDRVATDGKVDGAVGTLMT 292 Query: 276 GSRIDAVVERAGGRVVRIPLGQPHDGIKRYKAIFAAE-PWKLVHPKFGPWI--------D 326 ++ ++ AG + VR +G RY E W+L G + D Sbjct: 293 NMAVEVALQEAGVKFVRAAVGD------RYVLEQLREHGWQLGAEGSGHILSLDRHSTGD 346 Query: 327 PFVTMGLLIKLIDEN-GPLSELVKEIPTYYLKKANV-LCPD-EYK-AEVVRRAAEEVERK 382 V+ L++ + + L++L+ + + K NV + PD ++K ++ +RRA + E Sbjct: 347 GIVSALLVLAAMKRSEKTLADLLDGVTLFPQKLINVRMKPDADWKSSDAIRRAIAKAES- 405 Query: 383 LSSEIKEVLTISGFRIALNDGSWILIRPSGTEPKIRVVAEAPTEKRRDELFEMAYSTVSR 442 ALN +LIR SGTEP +RV+ EA E D L +++ Sbjct: 406 ----------------ALNGRGRVLIRASGTEPVLRVMVEA--ENAADAL--QYAESIAG 445 Query: 443 IVKEA 447 VKEA Sbjct: 446 AVKEA 450 Lambda K H 0.318 0.138 0.402 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: 498 Number of extensions: 24 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 450 Length of database: 452 Length adjustment: 33 Effective length of query: 417 Effective length of database: 419 Effective search space: 174723 Effective search space used: 174723 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 51 (24.3 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