Align phosphopentomutase (EC 5.4.2.7) (characterized)
to candidate SMc00637 SMc00637 phosphoglucosamine mutase
Query= BRENDA::Q6I7B6 (450 letters) >FitnessBrowser__Smeli:SMc00637 Length = 450 Score = 168 bits (426), Expect = 3e-46 Identities = 142/447 (31%), Positives = 227/447 (50%), Gaps = 51/447 (11%) Query: 2 RLFGTAGIRG-TLWEKVTPELAMKVGMAVGT-YKSG----KALVGRDGRTSSVMLKNAMI 55 R FGT GIRG + +TP+LAM+VG+AVGT +++G + ++G+D R S ML+NAM+ Sbjct: 4 RYFGTDGIRGQSNIFPMTPDLAMRVGIAVGTIFRNGAHRHRVVIGKDTRLSGYMLENAMV 63 Query: 56 SGLLSTGMEVLDADLIPTPALAWGTRKL-ADAGVMITASHNPPTDNGVKVFNGDGTEFYV 114 +G + G++V IPTP +A TR L AD GVMI+ASHN DNG+K+F DG + Sbjct: 64 AGFTAAGLDVFLLGPIPTPGVAMLTRSLRADIGVMISASHNAFRDNGIKLFGPDGYKLSD 123 Query: 115 EQERGLEEII---FSGNFRKARWDEIKPVRNVEV-IPDYINAVLDFVGHETNLK---VLY 167 + E+ +E+++ SG K ++I + V+ I YI + + LK + Sbjct: 124 DIEQKIEDLLEQDMSGQLAKP--EDIGRAKRVDGDIYRYIEQAKRTLPRDVTLKGLRIAI 181 Query: 168 DGANGAGSLVAPYLLREMGAKVLSVNAHVDGHFPGRKPEPRYENIAYLGKLVRELGVDLA 227 D ANGA VAP L E+GA+V+++ +G E + A L K V E+ D+ Sbjct: 182 DCANGAAYKVAPSALWELGAEVVTIGTEPNG--VNINLECGSTHPAALQKKVHEVRADIG 239 Query: 228 IAQDGDADRIAVFDEKGNYVDEDTVIALFAKLYVEEH--GGGTVVVSIDTGSRIDAVVER 285 IA DGDADR+ + DE+G +D D ++A+ A + + GG + ++ + ++ ++ Sbjct: 240 IALDGDADRVLIVDEEGAVIDGDQLMAVIADSWAADGMLKGGGIAATVMSNLGLERYLQA 299 Query: 286 AGGRVVRIPLGQPH-------DGIKRYKAIFAAEPWKLVHPKFGPWIDPFVTMGLLIKLI 338 ++ R +G + DG+ + + +V FG D V ++ ++ Sbjct: 300 RRLKLHRTKVGDRYVVEQMRQDGLN----VGGEQSGHIVLSDFGTTGDGLVAALQILAVV 355 Query: 339 DENG-PLSELVK--EIPTYYLKKANVLCPDEYKAEVVRRAAEEVERKLSSEIKEVLTISG 395 G +SE+ + E LK V + V++A E E +L+ + Sbjct: 356 KRQGKTVSEICRRFEPVPQVLKNVRVSAGKPLEDAAVQQAIAEAEAQLAKNGR------- 408 Query: 396 FRIALNDGSWILIRPSGTEPKIRVVAE 422 +LIRPSGTEP IRV+AE Sbjct: 409 ----------LLIRPSGTEPLIRVMAE 425 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: 491 Number of extensions: 28 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: 450 Length adjustment: 33 Effective length of query: 417 Effective length of database: 417 Effective search space: 173889 Effective search space used: 173889 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