Align phosphopentomutase (EC 5.4.2.7) (characterized)
to candidate AZOBR_RS07040 AZOBR_RS07040 phosphoglucosamine mutase
Query= BRENDA::Q6I7B6 (450 letters) >FitnessBrowser__azobra:AZOBR_RS07040 Length = 455 Score = 155 bits (391), Expect = 3e-42 Identities = 144/446 (32%), Positives = 214/446 (47%), Gaps = 41/446 (9%) Query: 3 LFGTAGIRGTL-WEKVTPELAMKVGMAVGT-YKSG----KALVGRDGRTSSVMLKNAMIS 56 LFGT GIRGT + +T E A++V MA ++ G + ++G+D R S +L+ A+ + Sbjct: 5 LFGTDGIRGTANIDPMTAETALRVAMASALQFRRGDHRHRVVIGKDTRLSGYLLEPALTA 64 Query: 57 GLLSTGMEVLDADLIPTPALAWGTRKL-ADAGVMITASHNPPTDNGVKVFNGDG------ 109 G +S GM+V+ +PTPA+A TR L AD GVMI+ASHNP DNG+K+F DG Sbjct: 65 GFISMGMDVVLLGPLPTPAVAMLTRSLRADLGVMISASHNPYQDNGIKLFGPDGYKLSDA 124 Query: 110 TEFYVEQERG---LEEIIFSGNFRKARWDEIKPVRNVEVIPDYINAVLDFVGHETNLKVL 166 E +E G ++ S + +A E R +E + + L G L+++ Sbjct: 125 VELAIETRMGQPFAPDLAGSADLGRASRLEDSTGRYIEYVKNTFPRGLRLDG----LRIV 180 Query: 167 YDGANGAGSLVAPYLLREMGAKVLSVNAHVDGHFPGRKPEPRYENIAYLGKLVRELGVDL 226 D ANGA VAP +L E+GA V+ V + DG + L + V G L Sbjct: 181 VDCANGAAYRVAPKVLYELGADVIPVGVNPDG--LNINKDCGATATRTLQEQVVAHGAHL 238 Query: 227 AIAQDGDADRIAVFDEKGNYVDEDTVIALFAKLYVEEH--GGGTVVVSIDTGSRIDAVVE 284 IA DGDADR+ + DE G VD D V+AL A + + GG VV ++ + ++ ++ Sbjct: 239 GIALDGDADRLIMVDEAGRVVDGDQVMALIASSWAQAQTLKGGGVVATVMSNLGMERHLQ 298 Query: 285 RAGGRVVRIPLGQPH--DGIKRY-KAIFAAEPWKLVHPKFGPWIDPFV-TMGLLIKLIDE 340 G +VR P+G + + ++ + + + +V + D + + +L LI Sbjct: 299 GLGIALVRTPVGDRYVVEHMREHGYNVGGEQSGHVVLSDYSTTGDGLIAALQVLAVLIQS 358 Query: 341 NGPLSELVKEIPTYYLKKANVLCPDEYKAEVVRRAAEEVERKLSSEIKEVLTISGFRIAL 400 G + V V P K VR AA +++S I L Sbjct: 359 GGRAASEV----------CQVFAPVPQKLTNVRFAAGSKPLEIAS---VQAAIRDGEARL 405 Query: 401 NDGSWILIRPSGTEPKIRVVAEAPTE 426 N ILIR SGTEP IRV+AE E Sbjct: 406 NGSGRILIRKSGTEPVIRVMAEGDDE 431 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: 484 Number of extensions: 28 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: 455 Length adjustment: 33 Effective length of query: 417 Effective length of database: 422 Effective search space: 175974 Effective search space used: 175974 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