Align Probable phosphoribomutase; PRM; Phosphoglucomutase 3 homolog; PGM 3 homolog; EC 5.4.2.7 (characterized)
to candidate 5210100 Shew_2544 phosphoglucomutase/phosphomannomutase alpha/beta/subunit (RefSeq)
Query= SwissProt::O74478 (587 letters) >FitnessBrowser__PV4:5210100 Length = 584 Score = 325 bits (833), Expect = 3e-93 Identities = 212/604 (35%), Positives = 308/604 (50%), Gaps = 43/604 (7%) Query: 1 MDPILQELVDEWFKLDQDETTRNEVSQLIKAEDYATLKQIMHPRIGFGTSGLRAEIGAGF 60 M +Q + W LD D +R E+ L+ L R+ FGT+G+R +GAG Sbjct: 1 MQTQIQARIKHWLSLDSDAKSRAEIQALVDQGAQEELVARFAGRLTFGTAGIRGVVGAGP 60 Query: 61 ARMNCLTVIQASQGFAEYLLQTVPSAAKLGVVIGHDHRHKSNTFARLTAAVFLQKGFKTY 120 RMN L V Q S+G AEYL V +A GVVIG+D RH S FA A+V GFK + Sbjct: 61 MRMNRLVVQQTSKGVAEYLKAQVENAVSRGVVIGYDGRHDSKQFAEDAASVLTAAGFKVF 120 Query: 121 FFDHLVHTPLVPFAVKTLGTAAGVMITASHNPAAYNGYKVYWGNGCAIIPPHDKGIAACI 180 + TPLV F V LG AAG+++TASHNP YNGYKVYWGNG IIPPHD GIAA I Sbjct: 121 LTSKVAPTPLVAFGVLHLGAAAGIVVTASHNPPQYNGYKVYWGNGAQIIPPHDTGIAARI 180 Query: 181 E------KNLTPITWDKNLVENHKLADRDFAVGLLKNYWSQLHEFHSENNFSLEMKS--- 231 E ++ P+ + VE KL +L+ + Q + N L+ + Sbjct: 181 ELAANSPVDMLPL---ETAVETGKLV-------MLEEDYYQAYRQGVLNAEVLQSPARPE 230 Query: 232 -LKFVYTPIHGVGLPFVTSALHLFGEQGDMISVPLQDSPNPDFPTVKFPNPEEEGALDLA 290 + YT +HGVG + L G + SV Q P+ DFPTV FPNPEE GA+ L Sbjct: 231 LVSLAYTAMHGVGAEMAETLLKDIGVT-QVYSVAAQREPDGDFPTVNFPNPEEAGAMVLV 289 Query: 291 YEQADANGISYVLATDPDADRFAFAEK---------INGAWRRFTGDEVGCILAYFIFQE 341 +A +G A DPDADRFA A + + A++ TGD+VG +L +++ Sbjct: 290 MAEAHKHGAMLACANDPDADRFAVAVRKPAATPEMLASEAYQMLTGDQVGVLLGHYLLSH 349 Query: 342 YKNVGKPIDDFYVLSTTVSSAMVKSMAKVEGFHHVETLTGFKWLGNKALELEKQGKFIGL 401 + D + T VSS+++ +++ G TLTGFKWL N + + Q Sbjct: 350 ASD-----DQRLLCCTIVSSSLLTRISEACGARCETTLTGFKWLTNVGMSKQTQENRFLF 404 Query: 402 AYEEALGYMVGSIVRDKDGVNALITFLHLLKRLQLQNLSITEVFEQMSKKYGYYTTQNSY 461 AYEEALGY VGS+V DKDG++AL+ F+ L L + ++ + E + ++YGYY + Sbjct: 405 AYEEALGYTVGSMVWDKDGLSALVAFVQLTAELAAKGETLWDRLETIYRQYGYYLNRQVS 464 Query: 462 FLSRDTPKLRALVDALRHYDTKSGYPATLGSKKITNVRDLTTGYDSSSTDGKATLPVSKS 521 P + + LR D P+ + + + +V D++ G + + T+ + + Sbjct: 465 IALSGEPGAPTIGEQLRALD-----PSEIAGRALVSVDDISLGVRRFADGREETIDLPR- 518 Query: 522 SDNVTFELENGEVIMTIRTSGTEPKLK-FYICARGHSLEDSIKNATEVKQAIKSEWFHPQ 580 SD + + L+ G + +R SGTEPK+K +Y ++ + + +A +E+ Sbjct: 519 SDVLIYRLQ-GNARVIVRPSGTEPKVKCYYEVVEPFGEQEGLADVQRRAEAAMAEFVSRH 577 Query: 581 QNGL 584 Q GL Sbjct: 578 QAGL 581 Lambda K H 0.318 0.135 0.401 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: 738 Number of extensions: 28 Number of successful extensions: 5 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: 587 Length of database: 584 Length adjustment: 37 Effective length of query: 550 Effective length of database: 547 Effective search space: 300850 Effective search space used: 300850 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 (21.7 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