Align Phosphoglucomutase-2; PGM 2; Glucose phosphomutase 2; Phosphodeoxyribomutase; Phosphoglucomutase-1; Phosphopentomutase; EC 5.4.2.2; EC 5.4.2.7 (characterized)
to candidate 7025556 Shewana3_2707 phosphoglucomutase/phosphomannomutase alpha/beta/subunit (RefSeq)
Query= SwissProt::Q7TSV4 (620 letters) >FitnessBrowser__ANA3:7025556 Length = 573 Score = 336 bits (861), Expect = 2e-96 Identities = 216/576 (37%), Positives = 299/576 (51%), Gaps = 45/576 (7%) Query: 19 MDARLDQETAQWLRWDQNPLTSESVKQLIAGGNKEELRKCFGARMEFGTAGLRAPMGAGI 78 M+ L + WL D +P T ++ LI GN EL F R+EFGTAGLR +GAG Sbjct: 1 MNTHLQLQVKHWLENDPDPRTQAQLQALIDAGNDAELEARFAGRLEFGTAGLRGVVGAGP 60 Query: 79 SRMNDLTIIQTTQGFCRYLEKQFSDLKQRGVVISFDARAHPASGGSSRRFARLAATAFIT 138 MN L I QT+ G YL +Q D +RGVVI +D R SR FA A+ Sbjct: 61 MGMNRLVIRQTSAGLGAYLLEQIKDAAERGVVIGYDGRH------DSRTFAHDTASVLTA 114 Query: 139 QGVPVYLFSDITPTPFVPYTVSHLKLCAGIMITASHNPKQDNGYKVYWDNGAQIISPHDR 198 G+ V L + + PTP V + V H AGI++TASHNP Q NGYKVYW+NGAQII PHD Sbjct: 115 MGIKVRLTAKVAPTPLVAFGVKHFNAAAGIVVTASHNPPQYNGYKVYWENGAQIIPPHDS 174 Query: 199 GISQAIEENLEPWPQAWEESLVDSSPLLHNPSAS-------IGNDYFEDLKKYCFHRTVN 251 GI+ I E + + P + A+ + +DY+E ++ H V Sbjct: 175 GIAAKI-----------ELAATQAIPFMDQVEATKQGKLIWLQDDYYETYRRGVMHANVL 223 Query: 252 KES----KVKFVHTSVHGVGHEFVQLAFKAFDLAPPEAVPQQKDPDPEFPTVKYPNPEEG 307 + + KV +T++HGVG E + K A +V Q++PD +FPTV +PNPEE Sbjct: 224 QNNTAPEKVSLAYTAMHGVGAEMAETVLKDAGFAQVYSVVAQREPDGDFPTVNFPNPEE- 282 Query: 308 KGVLTLSFALADKIKAKIVLANDPDADRLAVAEKQDSGEWRVFSGNELGALLGWWLFTSW 367 KG + L A A K A + ANDPDADR AVA ++D GE+++ +G+++G L G +L + Sbjct: 283 KGAMDLVIAEAKKHGAMLACANDPDADRFAVAVRKDDGEYQMLTGDQVGVLFGHYLLSHA 342 Query: 368 KEKNQDQSNLKDTYMLSSTVSSKILRAIALKEGFHFEETLTGFKWMGNRAQQLGDQGKTV 427 + + L T ++SS++ SKI + G TLTGFKW+ N Sbjct: 343 SK----EQRLVGTTIVSSSLLSKIAKGF----GVESYTTLTGFKWLMNVGIAQSQPDNQF 394 Query: 428 LFAFEEAIGYMCCPFVLDKDGVSAAVICAELASFLATKNLSLSQQLNAIYVEYGYHITTA 487 LFA+EEA+GY V DKDG+SA V A+L + LA K ++ +L IY E G+H+ A Sbjct: 395 LFAYEEALGYTVGNMVWDKDGLSALVAFAQLTAELAAKGQTIWDRLEQIYREQGFHL-NA 453 Query: 488 SYFICHDQGTIQNLFGNLRNYDGKNNYPKMCGKFEISAIRDLTTGYDDSQPDKKAVLPTS 547 I T N+ LR + P G+ + + DL + D K Sbjct: 454 QVSIALKPDT-PNIGAYLREHP-----PLAIGEHALVSTDDL-KALERRFADGKVEKINL 506 Query: 548 KSSQMITFTFANGGVATMRTSGTEPKIKYYAELCAP 583 +S ++T+ ANG +R SGTEPKIK Y E+ P Sbjct: 507 PASDVLTYRLANGARVIVRPSGTEPKIKCYYEVVEP 542 Lambda K H 0.317 0.133 0.403 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: 874 Number of extensions: 43 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: 620 Length of database: 573 Length adjustment: 37 Effective length of query: 583 Effective length of database: 536 Effective search space: 312488 Effective search space used: 312488 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: 53 (25.0 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