Align Phosphoglucomutase; PGM; Alpha-phosphoglucomutase; Glucose phosphomutase; EC 5.4.2.2 (characterized)
to candidate CA265_RS09660 CA265_RS09660 phosphoglucomutase
Query= SwissProt::P18159 (581 letters) >FitnessBrowser__Pedo557:CA265_RS09660 Length = 578 Score = 483 bits (1242), Expect = e-140 Identities = 253/545 (46%), Positives = 357/545 (65%), Gaps = 11/545 (2%) Query: 34 LEDCFYKDLEFGTGGMRGEIGAGTNRMNIYTVRKASAGFAAYISKQGEEAKKRGVVIAYD 93 L D FY+ LEFGTGG+RG +GAG+NR+N YT+ A+ G A Y++ + K + V IA+D Sbjct: 40 LTDAFYRSLEFGTGGLRGIMGAGSNRINKYTIGTATQGLANYLNNKYPNEKIK-VAIAHD 98 Query: 94 SRHKSPEFAMEAAKTLATQGIQTYVFDELRPTPELSFAVRQLNAYGGIVVTASHNPPEYN 153 SR+ S FA A + GI Y F LRPTPELSFAVR G+++TASHNP EYN Sbjct: 99 SRNNSDYFAKITADVFSANGIHVYFFSALRPTPELSFAVRHFGCKSGVMLTASHNPKEYN 158 Query: 154 GYKVYGDDGGQLPPKEADIVIEQVNAIENELTITVDEENKLKEKGLIKIIGEDIDKVYTE 213 GYK YG DGGQ + +VI++VN I+N +DE + + I++IGE++DK+Y + Sbjct: 159 GYKAYGADGGQFTSPDDKLVIDEVNKIKN-----IDEVKFDRVEANIELIGEEVDKLYLD 213 Query: 214 KLTSISVHPE-LSEEVDVKVVFTPLHGTANKPVRRGLEALGYKNVTVVKEQELPDSNFST 272 +T++S+ PE + + D+K+V++P+HGT V + L G+ NVT+V+EQ PD NF T Sbjct: 214 GITALSISPEAIKRQHDLKIVYSPIHGTGITLVPKALAQFGFTNVTLVEEQSTPDGNFPT 273 Query: 273 VTSPNPEEHAAFEYAIKLGEEQNADILIATDPDADRLGIAVKNDQGKYTVLTGNQTGALL 332 V PNPEE A A+ +E +AD+++ATDPDADR+GIAVK++ G++ +L GNQTG LL Sbjct: 274 VVYPNPEEKDALTLAMNKAKEIDADLVLATDPDADRVGIAVKDNNGEWVLLNGNQTGCLL 333 Query: 333 LHYLLSEKKKQGILPDNGVVLKTIVTSEIGRAVASSFGLDTIDTLTGFKFIGEKIKEYEA 392 ++YLLS + G L N ++KTIVTS + +A + +TLTGFK+IG+ + E E Sbjct: 334 INYLLSAWEANGKLDGNQFIVKTIVTSNLIEEIAKKKDVTYYNTLTGFKYIGQLMTELE- 392 Query: 393 SGQYTFQFGYEESYGYLIGDFARDKDAIQAALLAVEVCAFYKKQGMSLYEALINLFNEYG 452 G+ F G EESYGYLIGD RDKDA+ +A E+ A+YK +G SLY AL++++ EYG Sbjct: 393 -GKKYFIGGGEESYGYLIGDLVRDKDAVVSAAFISEMTAYYKDKGASLYNALLDMYVEYG 451 Query: 453 FYREGLKSLTLKGKQGAEQIEAILASFRQNPPQKMAGKQVVTAEDYAVSKRTLLTESKEE 512 Y+E L SLT KGK GAE+I+A++ FR+NPP + G +V +DY +S+ T LT K Sbjct: 452 LYKEDLVSLTKKGKSGAEEIKAMMVKFRENPPATLGGSKVSVLKDYELSQETDLTTGKVS 511 Query: 513 AIDLPKSNVLKYFLEDGSWFCLRPSGTEPKVKFYFAVKG--SSLEDSEKRLAVLSEDVMK 570 +D P S+VL++ EDGS RPSGTEPK+KFY +V + +D E A L + + Sbjct: 512 KLDYPTSDVLQFITEDGSIVSARPSGTEPKIKFYCSVNAPLADRKDFESVNAQLGDKIKA 571 Query: 571 TVDEI 575 + ++ Sbjct: 572 VMADL 576 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: 890 Number of extensions: 33 Number of successful extensions: 5 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: 578 Length adjustment: 36 Effective length of query: 545 Effective length of database: 542 Effective search space: 295390 Effective search space used: 295390 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 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