Align phosphopentomutase (EC 5.4.2.7) (characterized)
to candidate 3609008 Dshi_2397 phosphoglucosamine mutase (RefSeq)
Query= BRENDA::Q6I7B6 (450 letters) >FitnessBrowser__Dino:3609008 Length = 447 Score = 165 bits (417), Expect = 3e-45 Identities = 147/468 (31%), Positives = 219/468 (46%), Gaps = 48/468 (10%) Query: 2 RLFGTAGIRGTL-WEKVTPELAMKVGMAVGTY------KSGKALVGRDGRTSSVMLKNAM 54 +LFGT G+RGT +T E+A+++G A G Y + + ++G+D R S M + A+ Sbjct: 4 KLFGTDGVRGTANTAPMTAEMALRLGAAAGRYFRRDQSAAHRVVIGKDTRLSGYMFETAL 63 Query: 55 ISGLLSTGMEVLDADLIPTPALAWGTRKL-ADAGVMITASHNPPTDNGVKVFNGDGTEFY 113 +G STGM VL IPTPA+A T+ + AD GVMI+ASHNP DNG+K F DG + Sbjct: 64 TAGFTSTGMNVLLLGPIPTPAVALLTQSMRADVGVMISASHNPADDNGIKFFGPDGYKLS 123 Query: 114 VEQERGLEEIIFSGNFRKARWDEIKPVRNV-EVIPDYI-NAVLDFVGH--ETNLKVLYDG 169 E +EEI+ +G+ R A+ I + + + + YI A F H LKV+ D Sbjct: 124 DAAEEEIEEIL-AGDIRPAQAPNIGRAKRIDDGLGRYIERAKRTFPAHLRLDGLKVVVDC 182 Query: 170 ANGAGSLVAPYLLREMGAKVLSVNAHVDGHFPGRKPEPRYENIAYLGKLVRELGVDLAIA 229 ANGA VAP +L E+GA V+ V +G R A + V G D+ I Sbjct: 183 ANGAAYKVAPAVLWELGADVIPVGVSPNGRNINRDCGSTAPQTA--AEAVVSHGADVGIC 240 Query: 230 QDGDADRIAVFDEKGNYVDEDTVIALFAKLYVEEH--GGGTVVVSIDTGSRIDAVVERAG 287 DGDADR+ + DE G D D ++ALFA + + T+V ++ + ++ + G Sbjct: 241 LDGDADRVMILDENGELADGDQLMALFATRWAAQGLLRDNTLVATVMSNLGLEYYLNDLG 300 Query: 288 GRVVRIPLGQPHDGIKRYKA---IFAAEPWKLVHPKFGPWIDPFVT-MGLLIKLIDENGP 343 ++VR +G + K + + +V G D + + L +++ + Sbjct: 301 LKLVRTAVGDRYVVEAMRKGGWNLGGEQSGHIVMLDHGTTGDGLMAGLQFLAEMVQQGRS 360 Query: 344 LSELVKEIPTYYLKKANV---LCPDEYKAEVVRRAAEEVERKLSSEIKEVLTISGFRIAL 400 SEL T + NV D A V+ A E +LS + + Sbjct: 361 ASELKHSFTTVPQRLENVRFGAGQDPLAAASVKSAIAAAEAQLSGKGR------------ 408 Query: 401 NDGSWILIRPSGTEPKIRVVAEAPTEKRRDELFEMAYSTVSRIVKEAE 448 +LIR SGTEP +RV+AE E M S V +V E Sbjct: 409 -----LLIRKSGTEPLVRVMAECEDE-------AMLTSVVGEVVAAVE 444 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: 495 Number of extensions: 32 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: 450 Length of database: 447 Length adjustment: 33 Effective length of query: 417 Effective length of database: 414 Effective search space: 172638 Effective search space used: 172638 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