Align Phosphoglucomutase; PGM; Alpha-phosphoglucomutase; Glucose phosphomutase; EC 5.4.2.2 (characterized)
to candidate Echvi_2982 Echvi_2982 Phosphomannomutase
Query= SwissProt::P18159 (581 letters) >FitnessBrowser__Cola:Echvi_2982 Length = 575 Score = 446 bits (1148), Expect = e-130 Identities = 233/543 (42%), Positives = 339/543 (62%), Gaps = 15/543 (2%) Query: 15 HLDLELKERLIEL--EGDEQALEDCFYKDLEFGTGGMRGEIGAGTNRMNIYTVRKASAGF 72 ++D E K ++ +L D L D FYKDLEFGTGG+RG +G G+NRMN+YTV A+ G Sbjct: 17 NIDQESKTKIQQLLDASDSSELVDAFYKDLEFGTGGLRGVMGIGSNRMNVYTVGMATQGL 76 Query: 73 AAYISK--QGEEAKKRGVVIAYDSRHKSPEFAMEAAKTLATQGIQTYVFDELRPTPELSF 130 A Y+ GE+ K V I +DSR + FA A L GI+ F+E+RPTP LS+ Sbjct: 77 ANYLLACFPGEDIK---VAITHDSRINNTLFAETTANVLTANGIKVKYFEEMRPTPMLSY 133 Query: 131 AVRQLNAYGGIVVTASHNPPEYNGYKVYGDDGGQLPPKEADIVIEQVNAIENELTITVDE 190 A+R G+++TASHNP EYNGYK Y +DGGQ+ +I +V I++ +D+ Sbjct: 134 AIRHYGCKSGVMITASHNPKEYNGYKAYWEDGGQIVAPHDKNIIMEVQKIKS-----IDD 188 Query: 191 ENKLKEKGLIKIIGEDIDKVYTEKLTSISVHPE-LSEEVDVKVVFTPLHGTANKPVRRGL 249 K LI+ IG ++D Y + S+ P+ + + D+ +VF+P+HG + K V L Sbjct: 189 VKWDKNDALIEYIGAEMDLTYLNDIKKFSLSPKAILNQRDMCIVFSPIHGASGKMVPAAL 248 Query: 250 EALGYKNVTVVKEQELPDSNFSTVTSPNPEEHAAFEYAIKLGEEQNADILIATDPDADRL 309 + G++N+ VVKEQE PD F TV PNPEE A ++KL +E NA++++A DPD DR Sbjct: 249 KTFGFENIHVVKEQEAPDGTFPTVVYPNPEEAEALSLSLKLAKEVNAELVLACDPDGDRY 308 Query: 310 GIAVKNDQGKYTVLTGNQTGALLLHYLLSEKKKQGILPDNGVVLKTIVTSEIGRAVASSF 369 A+ N++G+Y +L GNQTG++L +YLL++ ++ G+ + ++ TIVT+E+ + F Sbjct: 309 AAAIPNEKGEYELLNGNQTGSILTYYLLNQWREHGLFTGDQFMVNTIVTTELIEEICHGF 368 Query: 370 GLDTIDTLTGFKFIGEKIKEYEASGQYTFQFGYEESYGYLIGDFARDKDAIQAALLAVEV 429 + LTGFK I I+E E G+ F G EESYG+L+GD RDKD + A + EV Sbjct: 369 NIPCYRVLTGFKNIAAIIRELE--GKKQFVGGGEESYGFLVGDAVRDKDGVSACAMLAEV 426 Query: 430 CAFYKKQGMSLYEALINLFNEYGFYREGLKSLTLKGKQGAEQIEAILASFRQNPPQKMAG 489 A+YK++GM+L++ L ++ YGFY+E L S+T KGK GAEQI+ ++ FR N P+ + G Sbjct: 427 VAYYKEKGMTLFDVLAEIYQSYGFYKESLISVTKKGKDGAEQIQQLMHGFRTNRPEAING 486 Query: 490 KQVVTAEDYAVSKRTLLTESKEEAIDLPKSNVLKYFLEDGSWFCLRPSGTEPKVKFYFAV 549 +VV D SK + + EE +DL KSNV++++LEDGS RPSGTEPK+K+Y +V Sbjct: 487 TKVVKVVDVKESKVYNIADGTEEDLDLDKSNVIQFYLEDGSKISARPSGTEPKIKYYISV 546 Query: 550 KGS 552 S Sbjct: 547 NES 549 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: 829 Number of extensions: 35 Number of successful extensions: 4 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: 575 Length adjustment: 36 Effective length of query: 545 Effective length of database: 539 Effective search space: 293755 Effective search space used: 293755 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