Align phosphopentomutase (EC 5.4.2.7) (characterized)
to candidate WP_013402170.1 CALHY_RS01030 phosphoglucosamine mutase
Query= BRENDA::Q6I7B6 (450 letters) >NCBI__GCF_000166355.1:WP_013402170.1 Length = 449 Score = 165 bits (417), Expect = 3e-45 Identities = 148/467 (31%), Positives = 231/467 (49%), Gaps = 46/467 (9%) Query: 2 RLFGTAGIRGTLWEKVTPELAMKVGMA-----VGTYKSGKALVGRDGRTSSVMLKNAMIS 56 +LFGT G+RG +++T ELA +G A T + K L+G+D R S ML+ A+ + Sbjct: 3 KLFGTDGVRGVANKELTCELAFDLGRAGAYVLTETKQKPKILIGKDTRISCDMLEAALCA 62 Query: 57 GLLSTGMEVLDADLIPTPALAWGTRKLA-DAGVMITASHNPPTDNGVKVFNGDGTEFYVE 115 GL S G +V A +I TPA+A + DAG+MI+ASHNP NG+K FN G + + Sbjct: 63 GLTSVGADVYLAGVITTPAIAHLVKSHGFDAGIMISASHNPYEFNGIKFFNSQGFKLSDQ 122 Query: 116 QERGLEEIIFSGNFRK---ARWDEIKPVRNVEV---IPDYINAVLDFVGHETNLKVLYDG 169 E +E+II + + + A++D I V V++ +Y+ + L+ + LK++ D Sbjct: 123 IEEKIEDIILNRKWNEVPHAQFDAIGRVNRVDLKKNYQEYLKSTLNGASFK-GLKIVIDC 181 Query: 170 ANGAGSLVAPYLLREMGAKVLSVNAHVDGHFPGRKPEPRYENIAYLGKLVRELGVDLAIA 229 ANGA +AP + E+GA+V+ +N DG E ++ L + V + D IA Sbjct: 182 ANGAAYKIAPEVFEELGAEVVVINNQPDG--TNINKECGSTHLKMLQQEVVKNKADFGIA 239 Query: 230 QDGDADRIAVFDEKGNYVDEDTVIALFAKLYVEEHG---GGTVVVSIDTGSRIDAVVERA 286 DGDADR DE+G+ VD D ++ L A+ +++ G T+VV++ + + + Sbjct: 240 YDGDADRTLFVDEEGSIVDGDKIMLLLAQ-NLKQQGKLQRNTLVVTVMSNMGLFVAAKEL 298 Query: 287 GGRVVRIPLGQPHDGIKRYK---AIFAAEPWKLVHPKFGPWIDPFVTMGLLIKLIDENG- 342 G + +G + K + +I + ++ F D +T L KLI E+G Sbjct: 299 GINLEVTKVGDRYVLEKMLEGGYSIGGEQSGHIILLDFATTGDGILTSLQLTKLIKESGK 358 Query: 343 PLSELVKEIPTYYLKKANVLC----PDEY-KAEVVRRAAEEVERKLSSEIKEVLTISGFR 397 LS+L K + Y N D Y K V+ A ++VE K Sbjct: 359 KLSDLAKIMKVYPQVLVNAKVENGKKDLYSKDPVILEAIKKVEEK--------------- 403 Query: 398 IALNDGSWILIRPSGTEPKIRVVAEAPT-EKRRDELFEMAYSTVSRI 443 LN +LIRPSGTEP IRV+ E E+ + + E+A SR+ Sbjct: 404 --LNGKGRVLIRPSGTEPLIRVMIEGEDYEEIKKDAHELASLIESRL 448 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: 475 Number of extensions: 29 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: 449 Length adjustment: 33 Effective length of query: 417 Effective length of database: 416 Effective search space: 173472 Effective search space used: 173472 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