Align Probable phosphoribomutase; PRM; Phosphoglucomutase 3 homolog; PGM 3 homolog; EC 5.4.2.7 (characterized)
to candidate WP_101589167.1 BJEO58_RS09135 phospho-sugar mutase
Query= SwissProt::O74478 (587 letters) >NCBI__GCF_900169175.1:WP_101589167.1 Length = 617 Score = 250 bits (639), Expect = 1e-70 Identities = 204/591 (34%), Positives = 277/591 (46%), Gaps = 84/591 (14%) Query: 7 ELVDEWFKLDQDETTRNEVSQLIKA----------EDYATLKQIMHPRIGFGTSGLRAEI 56 ++V W D D TR E+S+L++A E A L + FGT+GLR EI Sbjct: 14 DVVRAWIADDPDPVTRAELSELLEAATAEAGPASAEALADLTDRFSGPLEFGTAGLRGEI 73 Query: 57 GAGFARMNCLTVIQASQGFAEYLLQTVPSAAK-----LGVVIGHDHRHKSNTFARLTAAV 111 AG RMN VI+A+ G + +L + + VVIG D R+ S FAR TAAV Sbjct: 74 AAGPHRMNRAVVIRAAAGLSAFLADHMQDSGPAISQPFTVVIGCDARYGSADFARDTAAV 133 Query: 112 FLQKGFKTYFFDHLVHTPLVPFAVKTLGTAAGVMITASHNPAAYNGYKVYWGN------- 164 G + + TP++ FAV+ LG AGVM+TASHNP NGYKVY G Sbjct: 134 VTAAGGRALLLPAKLPTPVLAFAVQHLGADAGVMVTASHNPPRDNGYKVYLGTRPLIALD 193 Query: 165 ---------GCAIIPPHDKGIAACIEKNLTPITWDKNLVENHKLADRDF-AVG--LLKNY 212 G I+PP D+ IA+ I + V + AD + ++G + Y Sbjct: 194 GPEQAAHGTGAQIVPPADELIASRIAA--------VDAVASVPRADSGWTSLGSEVETAY 245 Query: 213 WSQLHEFHSENNFSLEMKSLKFVYTPIHGVGLPFVTSALHLFGEQGDMISVPLQDSPNPD 272 L +E ++ +L+ V T +HGVG + AL G D+ V Q P+PD Sbjct: 246 LDSLTRLGAE---AVPRGALRIVTTALHGVGATTLARALGKAGF-ADVRPVESQRDPDPD 301 Query: 273 FPTVKFPNPEEEGALDLAYEQADANGISYVLATDPDADRFAFA--EKINGAWRRFTGDEV 330 FPTV FPNPEE+GAL+ A AD +LA DPDADR + A W + +GDEV Sbjct: 302 FPTVAFPNPEEDGALEEATALADHVDAHLILANDPDADRLSAAVPSPDGSGWYQLSGDEV 361 Query: 331 GCILAYFIFQEYKNVGKPIDD--------FYVLSTTVSSAMVKSMAKVEGFHHVETLTGF 382 G +L I P++D S+ VSS + ++A G H TLTGF Sbjct: 362 GLLLGEAIALRLAEAAAPLEDPAAQPALHPVFASSVVSSRALAALAARHGIAHTPTLTGF 421 Query: 383 KWLGNKALELEKQGKFIGLAYEEALGYMVG-SIVRDKDGVNALITFLHLLKRLQLQNLSI 441 KW+ + I YEEALGY V VRDKDG++A + F RL+ +I Sbjct: 422 KWI--------SRVPGIVYGYEEALGYCVDPDTVRDKDGISAALLFAAYTSRLRAAGRTI 473 Query: 442 TEVFEQMSKKYGYYTTQNSYFLSRDTPKLRALVDALRHYDTKSGYPATLGSKKITNVRDL 501 + ++ G + TQ F DT + V LR + P LG +T V D+ Sbjct: 474 PDELARIRATDGVFRTQPLTFRLEDTALIAGAVATLR-----ANPPTQLGGSPVTEVIDM 528 Query: 502 TTGY-DSSSTDGKATLPVSKSSDNVTFELENGEVIMTIRTSGTEPKLKFYI 551 T GY D + TDG L +++ D +R SGTEPKLK Y+ Sbjct: 529 TLGYGDLAPTDGIVVL--TQAGDRA-----------IVRPSGTEPKLKCYL 566 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: 818 Number of extensions: 38 Number of successful extensions: 10 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 587 Length of database: 617 Length adjustment: 37 Effective length of query: 550 Effective length of database: 580 Effective search space: 319000 Effective search space used: 319000 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