Align Phosphoglucomutase; PGM; Alpha-phosphoglucomutase; Glucose phosphomutase; EC 5.4.2.2 (characterized)
to candidate WP_013444375.1 PALPR_RS04220 phospho-sugar mutase
Query= SwissProt::P18159 (581 letters) >NCBI__GCF_000183135.1:WP_013444375.1 Length = 582 Score = 459 bits (1182), Expect = e-133 Identities = 243/532 (45%), Positives = 346/532 (65%), Gaps = 10/532 (1%) Query: 23 RLIELEGDEQALEDCFYKDLEFGTGGMRGEIGAGTNRMNIYTVRKASAGFAAYISKQGEE 82 RL+E E D+ L + FY+DLEFGTGG+RG +G GTNRMNIYTV A+ G + Y+ Q + Sbjct: 32 RLLEAE-DKSELIESFYRDLEFGTGGLRGIMGVGTNRMNIYTVGAATQGLSNYLKAQFPD 90 Query: 83 AKKRGVVIAYDSRHKSPEFAMEAAKTLATQGIQTYVFDELRPTPELSFAVRQLNAYGGIV 142 + VVI +D R+ S F+ +A + GI+ Y+F++LRPTPE SFA+R L GI+ Sbjct: 91 VPQLSVVIGHDCRNNSRLFSEISANIFSANGIKVYLFEDLRPTPEASFAIRHLGCQSGII 150 Query: 143 VTASHNPPEYNGYKVYGDDGGQLPPKEADIVIEQVNAIENELTITVDEENKLKEKGLIKI 202 +TASHNP EYNGYK Y +DG Q+ + VI +VN I + VD+ LI+I Sbjct: 151 LTASHNPKEYNGYKAYWNDGAQMVAPHDENVITEVNKIAS-----VDDIKFEGNPALIEI 205 Query: 203 IGEDIDKVYTEKLTSISVHPE-LSEEVDVKVVFTPLHGTANKPVRRGLEALGYKNVTVVK 261 IGE+IDK++ E + +S+ PE + ++K+V+TP+HGT K + R L+ G+ N+ V Sbjct: 206 IGEEIDKLFIENIKKLSLSPESIKRNSNLKIVYTPIHGTGVKLIPRALKEYGFTNIIAVP 265 Query: 262 EQELPDSNFSTVTSPNPEEHAAFEYAIKLGEEQNADILIATDPDADRLGIAVKNDQGKYT 321 EQ + NF TV SPNPEE AA + A+K E +ADI++A+DPDADRLGIAVKND+G++ Sbjct: 266 EQNVVSGNFPTVVSPNPEEPAALDMAVKKAIETDADIVMASDPDADRLGIAVKNDKGEWI 325 Query: 322 VLTGNQTGALLLHYLLSEKKKQGILPDNGVVLKTIVTSEIGRAVASSFGLDTIDTLTGFK 381 ++ GNQT L ++YL+ K+ G L N ++KTIVT+EI + +A G++ D TGFK Sbjct: 326 LVNGNQTALLFIYYLIRRWKELGKLNGNQYIVKTIVTTEIIKQIAERNGVEMFDCFTGFK 385 Query: 382 FIGEKIKEYEASGQYTFQFGYEESYGYLIGDFARDKDAIQAALLAVEVCAFYKKQGMSLY 441 +I I+E E +Y G EESYG+L +FARDKDA+ + + E+ A+ K G +L+ Sbjct: 386 WIAAVIRENEGKKEYI--GGGEESYGFLPEEFARDKDAVSSCTVMAEIAAWAKDNGKTLF 443 Query: 442 EALINLFNEYGFYREGLKSLTLKGKQGAEQIEAILASFRQNPPQKMAGKQVVTAEDYAVS 501 E L +++ EYG+ +E S+ KGK GAE+I ++ FR NPP+++AG +V +DY Sbjct: 444 ELLQDIYVEYGYGKEKGISVVRKGKSGAEEIAQMMRDFRSNPPKEIAGSKVKVVKDYDSL 503 Query: 502 KRTLLTESKEEAIDLP-KSNVLKYFLEDGSWFCLRPSGTEPKVKFYFAVKGS 552 K T L K + +P SNVL+YF EDG+ +RPSGTEPK+KFY V+G+ Sbjct: 504 KMTDLDSGKVSDLIMPATSNVLQYFTEDGTKISVRPSGTEPKIKFYIEVRGA 555 Lambda K H 0.313 0.133 0.371 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: 846 Number of extensions: 34 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: 581 Length of database: 582 Length adjustment: 36 Effective length of query: 545 Effective length of database: 546 Effective search space: 297570 Effective search space used: 297570 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 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