Align Probable phosphoribomutase; PRM; Phosphoglucomutase 3 homolog; PGM 3 homolog; EC 5.4.2.7 (characterized)
to candidate 6937015 Sama_1189 phosphoglucomutase/phosphomannomutase family protein (RefSeq)
Query= SwissProt::O74478 (587 letters) >FitnessBrowser__SB2B:6937015 Length = 585 Score = 315 bits (807), Expect = 3e-90 Identities = 207/565 (36%), Positives = 283/565 (50%), Gaps = 32/565 (5%) Query: 1 MDPILQELVDEWFKLDQDETTRNEVSQLIKAEDYATLKQIMHPRIGFGTSGLRAEIGAGF 60 MD L V W D D +R + L+ A D L+ R+ FGT+G+R +G G Sbjct: 1 MDTQLAFKVKHWLARDPDAKSRAALEALVAAGDDRALEAAFDGRLAFGTAGIRGIVGPGP 60 Query: 61 ARMNCLTVIQASQGFAEYLLQTVPSAAKLGVVIGHDHRHKSNTFARLTAAVFLQKGFKTY 120 MN L V + S G YL + A + G+VIG D RH S FA A V GFK Sbjct: 61 MGMNRLLVRETSAGLGAYLEAQIKDAKRRGLVIGFDGRHDSRVFAHDAACVLSAMGFKVR 120 Query: 121 FFDHLVHTPLVPFAVKTLGTAAGVMITASHNPAAYNGYKVYWGNGCAIIPPHDKGIAACI 180 H+ TPLV F VK AAG+++TASHNP YNGYKVYW NG IIPPHD GIAACI Sbjct: 121 LTSHVAPTPLVAFGVKHFEAAAGIVVTASHNPPKYNGYKVYWENGAQIIPPHDAGIAACI 180 Query: 181 EK--NL-TPITWDKNLVENHKLA--DRDFAVGLLKNYWSQLHE--FHSENNFSLEMKSLK 233 ++ NL P + V+ +L+ DF + + LH H SL Sbjct: 181 DRAANLELPWMPEPEAVKQGRLSFLQDDFFERYRR---AILHSPLLHPAGESQAGRASLG 237 Query: 234 FVYTPIHGVGLPFVTSALHLFGEQGDMISVPLQDSPNPDFPTVKFPNPEEEGALDLAYEQ 293 YT +HGVG P L G + SV Q P+ +FPTV FPNPEE GA+D+ + Sbjct: 238 IAYTAMHGVGAPMAERVLRDAG-FSQVYSVAAQREPDGNFPTVNFPNPEEPGAMDMVIAE 296 Query: 294 ADANGISYVLATDPDADRFAF-AEKINGAWRRFTGDEVGCILAYFIFQEYKNVGKPIDDF 352 A G A DPDADRFA A + +G +R +GD+ G +L ++ ++ G P+ Sbjct: 297 AGDKGALLACANDPDADRFALAARQSDGGYRMLSGDQTGALLCDYLLSHWQGAGVPL--- 353 Query: 353 YVLSTTVSSAMVKSMAKVEGFHHVETLTGFKWLGNKALELEKQGKFIGLAYEEALGYMVG 412 V +T VSSA++ ++A G H TLTGFKWL N A +LE + AYEEALGY VG Sbjct: 354 -VGNTIVSSALLHAIAAHYGAHSYTTLTGFKWLMNTAQQLETPQQPFLFAYEEALGYTVG 412 Query: 413 SIVRDKDGVNALITFLHLLKRLQLQNLSITEVFEQMSKKYGYYTT-QNSYFLSRDTPKLR 471 ++V DKDG++A + F +L L + + E++ +++G Y Q S L TP + Sbjct: 413 NLVWDKDGISAQLCFANLAAELLAEGKDVWAALERLYRRHGLYVNRQVSIALGEGTPDIG 472 Query: 472 ALVDALRHYDTKSGYPATLGSKKITNVRDLTTGYDSSSTDGKATLPVSKSSDNVTFELEN 531 A + + P + + + DL DG+ +SD + + L Sbjct: 473 AWL--------RDNPPTEIDKRPVVAREDLKR-LRKVYADGREEEIALPASDVLIYHLGA 523 Query: 532 GEVI------MTIRTSGTEPKLKFY 550 + + +R SGTEPK+K Y Sbjct: 524 SDATPGSTARVIVRPSGTEPKIKCY 548 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: 805 Number of extensions: 36 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: 587 Length of database: 585 Length adjustment: 37 Effective length of query: 550 Effective length of database: 548 Effective search space: 301400 Effective search space used: 301400 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