Align phosphopentomutase (EC 5.4.2.7) (characterized)
to candidate WP_011373653.1 SUDEN_RS10580 phosphoglucosamine mutase
Query= BRENDA::Q6I7B6 (450 letters) >NCBI__GCF_000012965.1:WP_011373653.1 Length = 446 Score = 163 bits (412), Expect = 1e-44 Identities = 140/458 (30%), Positives = 228/458 (49%), Gaps = 44/458 (9%) Query: 1 MRLFGTAGIRGTLWEKVTPELAMKVGMAVGTYK-----SGKALVGRDGRTSSVMLKNAMI 55 M+LFGT G+RG +T ELAM+V MA G Y + K LVG+D R S M++NA++ Sbjct: 1 MKLFGTDGVRGEAGTFLTAELAMRVAMAAGIYFKAHSITNKILVGKDTRRSGYMIENAIV 60 Query: 56 SGLLSTGMEVLDADLIPTPALAWGTRKL-ADAGVMITASHNPPTDNGVKVFNGDGTEFYV 114 SGL + G +V+ +PTPA+A+ T + DAG+MI+ASHN DNG+K F+G G + Sbjct: 61 SGLTAIGYDVIQIGPMPTPAIAFITENMRCDAGIMISASHNSFEDNGIKFFDGRGDKLPH 120 Query: 115 EQERGLEEIIFSGNFRKARWDEIKPV----RNVEVIPDYINAVLDFVGHETNLK---VLY 167 E +E+I F + + K + R +VI YI + + + +LK ++ Sbjct: 121 SVEEEIEKIFFDKDTILEAQTQGKYIGKAKRIDDVIGRYIVQLKNSFPRDLSLKDMRIVL 180 Query: 168 DGANGAGSLVAPYLLREMGAKVLSVNAHVDGHFPGRKPEPRYENIAYLGKLVRELGVDLA 227 D ANGAG +V P +L E+GA+V+ ++ DG + + + V + DL Sbjct: 181 DAANGAGYMVGPTVLEELGAEVIVLHNKPDGF--NINDSCGALHTKDVCESVVKYRADLG 238 Query: 228 IAQDGDADRIAVFDEKGNYVDEDTVIALFAKLYVEEHG---GGTVVVSIDTGSRIDAVVE 284 IA DGDADR+ + DE G VD D ++ ++ + G GG +V ++ + +D + Sbjct: 239 IALDGDADRVVIVDENGVVVDGDQLLGALG-AFMSDRGTLKGGGIVSTVMSNRGLDDFMS 297 Query: 285 RAGGRVVRIPLGQPH--DGIKRYKAIFAAE-PWKLVHPKFGPWIDPFVT-MGLLIKLIDE 340 G ++ R +G + + +K+ F E ++ F D V+ + +L L+ Sbjct: 298 DKGLKLFRSDVGDKNVLEVMKKEGINFGGEQSGHVIISDFAKTGDGLVSALQVLALLLKT 357 Query: 341 NGPLSELVKEIPTYYLKKANVLCPDEYKAEVVRRAAEEVERKLSSEIKEVLTISGFRIAL 400 + S+ ++ Y K N+ + K + V + ++ KL E+ E Sbjct: 358 SQKASKALRPFALYPQKLVNI----KVKTKKVLSEIDGLDEKL-KELDE----------- 401 Query: 401 NDGSWILIRPSGTEPKIRVVAEAPTEKR----RDELFE 434 +G L+R SGTE K+RV+ E K+ DE+ E Sbjct: 402 -NGVHHLVRYSGTENKLRVLLECKDAKKMNLYMDEMVE 438 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: 489 Number of extensions: 33 Number of successful extensions: 6 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: 446 Length adjustment: 33 Effective length of query: 417 Effective length of database: 413 Effective search space: 172221 Effective search space used: 172221 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 24 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