Align Probable phosphoribomutase; PRM; Phosphoglucomutase 3 homolog; PGM 3 homolog; EC 5.4.2.7 (characterized)
to candidate WP_017257613.1 B176_RS0104620 phospho-sugar mutase
Query= SwissProt::O74478 (587 letters) >NCBI__GCF_000302595.1:WP_017257613.1 Length = 578 Score = 298 bits (763), Expect = 4e-85 Identities = 190/554 (34%), Positives = 294/554 (53%), Gaps = 16/554 (2%) Query: 1 MDPILQELVDEWFKLDQDETTRNEVSQLIKAEDYATLKQIMHPRIGFGTSGLRAEIGAGF 60 +D Q+ V++W + DE T+ E+ L+ + L + + FGT GLR +GAG Sbjct: 4 LDKATQDRVNQWLNGNYDEATKAEIKALVDSNAVTELTDSFYKSLEFGTGGLRGIMGAGS 63 Query: 61 ARMNCLTVIQASQGFAEYLLQTVPSAAKLGVVIGHDHRHKSNTFARLTAAVFLQKGFKTY 120 R+N T+ A+QG A YL+ P K+ V I HD R+ S+ ++TA VF G Y Sbjct: 64 NRVNKYTIGAATQGLANYLINKYPGE-KIKVAIAHDSRNNSDVLGKITADVFSANGIHVY 122 Query: 121 FFDHLVHTPLVPFAVKTLGTAAGVMITASHNPAAYNGYKVYWGNGCAIIPPHDKGIAACI 180 FF L TP + FAV+TLG +GVM+TASHNP YNGYK Y +G + P D+ + + Sbjct: 123 FFKALRPTPELSFAVRTLGCKSGVMLTASHNPKEYNGYKAYGEDGGQFVAPDDQLVMDEV 182 Query: 181 EK--NLTPITWDKNLVENHKLADRDFAVGLLKNYWSQLHEFHSENNFSLEMKSLKFVYTP 238 K ++ I +D EN + + ++Y +++ + K LK V++P Sbjct: 183 AKVESVDDIKFDAK-PENISYIGEE----MDEDYLNKITSLSVSPDAIKRQKDLKIVFSP 237 Query: 239 IHGVGLPFVTSALHLFGEQGDMISVPLQDSPNPDFPTVKFPNPEEEGALDLAYEQADANG 298 IHG G+ V +AL FG + ++I V Q +P+ DFPTV +PNPEE+ AL LA ++A Sbjct: 238 IHGTGITLVPAALKRFGFE-NVILVEEQTTPDGDFPTVVYPNPEEKEALTLALKKAKETD 296 Query: 299 ISYVLATDPDADRFAFAEK-INGAWRRFTGDEVGCILAYFIFQEYKNVGKPIDDFYVLST 357 V+ATDPDADR A K + G + G++ G +L ++ + ++ GK YV+ T Sbjct: 297 ADLVMATDPDADRVGIAVKNLKGEFELLNGNQTGSLLINYMLEAWEKEGKFTGKEYVIKT 356 Query: 358 TVSSAMVKSMAKVEGFHHVETLTGFKWLGNKALELEKQGKFIGLAYEEALGYMVGSIVRD 417 V+S ++ +A + TLTGFK++G ELE + FI + EE+ GY+VG VRD Sbjct: 357 IVTSYLIDKIAADKKVKCYNTLTGFKFIGQIMTELEGKETFI-VGGEESYGYLVGDFVRD 415 Query: 418 KDGVNALITFLHLLKRLQLQNLSITEVFEQMSKKYGYYTTQNSYFLSRDTPKLRALVDAL 477 KD V + + + Q S+ E M KYG+Y + + +V + Sbjct: 416 KDAVVSAAFIAEMTAFYKDQGSSLYEAMINMYVKYGFYKEKLVSITKKGKSGAEEIVAMM 475 Query: 478 RHYDTKSGYPATLGSKKITNVRDLTTGYDSSSTDGKAT-LPVSKSSDNVTFELENGEVIM 536 + ++ P +LG K+ ++D +++ D + +P+ K SD + F E+G I+ Sbjct: 476 ERF--RNNPPKSLGGSKVVTLKDYGQRKETNLVDNTTSEIPLPK-SDVLQFITEDG-CII 531 Query: 537 TIRTSGTEPKLKFY 550 + R SGTEPK+KFY Sbjct: 532 SARPSGTEPKIKFY 545 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: 819 Number of extensions: 51 Number of successful extensions: 7 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: 578 Length adjustment: 36 Effective length of query: 551 Effective length of database: 542 Effective search space: 298642 Effective search space used: 298642 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 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