Align Probable phosphoribomutase; PRM; Phosphoglucomutase 3 homolog; PGM 3 homolog; EC 5.4.2.7 (characterized)
to candidate WP_033101249.1 JG50_RS0111465 phospho-sugar mutase
Query= SwissProt::O74478 (587 letters) >NCBI__GCF_000763315.1:WP_033101249.1 Length = 565 Score = 253 bits (647), Expect = 1e-71 Identities = 189/572 (33%), Positives = 284/572 (49%), Gaps = 47/572 (8%) Query: 18 DETTRNEVSQLIKAEDYATLKQIMHPRIGFGTSGLRAEIGAGFARMNCLTVIQASQGFAE 77 DE T+ E+S L D ++ + + FGT G+R IGAG R+N T+ + + G A Sbjct: 17 DEKTKLELSMLT---DEKEIEDRFYQDLKFGTGGVRGLIGAGTNRINLYTIRKITCGLAN 73 Query: 78 YLLQTVPSAAKL-GVVIGHDHRHKSNTFARLTAAVFLQKGFKTYFFDHLVHTPLVPFAVK 136 YL AK GV I D R S+ FA+ A V G K + FD L+ TP++ F VK Sbjct: 74 YLQAEFGEQAKRQGVAIAFDSRLNSSAFAKEAALVLCATGIKVFLFDRLMPTPVLSFTVK 133 Query: 137 TLGTAAGVMITASHNPAAYNGYKVYWGNGCAIIPPHDKGIAACIEKNLTPITWDKNLVEN 196 LG AG++ITASHNP YNGYKVY GC ++P + I ++ +T +T K V N Sbjct: 134 HLGCIAGIVITASHNPKDYNGYKVYDNKGCQLVPRYTDRITRYVDA-VTDLT--KISVAN 190 Query: 197 HKLADRDFAVGLLKNYWSQLHEFHSEN-------NFSLEMKSLKFVYTPIHGVGLPFVTS 249 ++ A A G+LK +++ + + + + +LK VYTP+HG G V S Sbjct: 191 YEQA---MAEGMLKIIGTEVLDAFIDEVLMQTCFDDADAKAALKIVYTPLHGTGNLPVRS 247 Query: 250 ALHLFGEQGDMISVPLQDSPNPDFPTVKFPNPEEEGALDLAYEQADANGISYVLATDPDA 309 L G G + V Q+ P+ F TV PNPE+ AL+L EQA A G VL TDPD Sbjct: 248 VLERDGFTGVSV-VKAQEFPDSSFSTVSSPNPEDRSALELGIEQAIAGGDDIVLGTDPDC 306 Query: 310 DRFAFAEKINGAWRRFTGDEVGCILAYFIFQEYKNVGKPIDDFYVLSTTVSSAMVKSMAK 369 DR A + + TG+++G +L +F+ + K+ + ++ T V+ + +A+ Sbjct: 307 DRVGVAVRSGEGFTLLTGNQIGALLVHFVLSQRKHALN--EKSTLVKTIVTDELGAKIAQ 364 Query: 370 VEGFHHVETLTGFKWLGNKALELEKQGK---FIGLAYEEALGYMVGSIVRDKDGVNALIT 426 G + V+TLTGFK++G++ E+ G+ FIG YEE+ G++VG RDKD + A + Sbjct: 365 SYGLNIVDTLTGFKYIGDQITLYEQTGEKEFFIG--YEESYGFLVGMHARDKDAIVASML 422 Query: 427 FLHLLKRLQLQNLSITEVFEQMSKKYGYYTTQNSYFLSR---DTPKLRALVDALRHYDTK 483 + + Q ++ V + + YGYY F ++++++ LR+ T Sbjct: 423 ICEMAAYYKTQGKTLLNVLSDIYEHYGYYFNAIDSFEFNGKVGVEEMQSMMTTLRNKGT- 481 Query: 484 SGYPATLGSKKITNVRDLTTGYDSSSTDGKATLPVSKSSDNVTFELENGEVIMTIRTSGT 543 TL I +RD +TG D LP S NV + N + IR SGT Sbjct: 482 -----TL-ITGIIEIRDYSTGIDG--------LPKS----NVLKYILNDGSWIAIRPSGT 523 Query: 544 EPKLKFYICARGHSLEDSIKNATEVKQAIKSE 575 EPK+K Y + K ++ I+ E Sbjct: 524 EPKIKVYYSVYQPDAYSAQKRLEMIQTTIRKE 555 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: 753 Number of extensions: 41 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: 565 Length adjustment: 36 Effective length of query: 551 Effective length of database: 529 Effective search space: 291479 Effective search space used: 291479 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