Align Phosphoglucomutase; PGM; Alpha-phosphoglucomutase; Glucose phosphomutase; EC 5.4.2.2 (characterized)
to candidate 6937015 Sama_1189 phosphoglucomutase/phosphomannomutase family protein (RefSeq)
Query= SwissProt::P18159 (581 letters) >FitnessBrowser__SB2B:6937015 Length = 585 Score = 313 bits (801), Expect = 2e-89 Identities = 207/555 (37%), Positives = 292/555 (52%), Gaps = 25/555 (4%) Query: 29 GDEQALEDCFYKDLEFGTGGMRGEIGAGTNRMNIYTVRKASAGFAAYISKQGEEAKKRGV 88 GD++ALE F L FGT G+RG +G G MN VR+ SAG AY+ Q ++AK+RG+ Sbjct: 32 GDDRALEAAFDGRLAFGTAGIRGIVGPGPMGMNRLLVRETSAGLGAYLEAQIKDAKRRGL 91 Query: 89 VIAYDSRHKSPEFAMEAAKTLATQGIQTYVFDELRPTPELSFAVRQLNAYGGIVVTASHN 148 VI +D RH S FA +AA L+ G + + + PTP ++F V+ A GIVVTASHN Sbjct: 92 VIGFDGRHDSRVFAHDAACVLSAMGFKVRLTSHVAPTPLVAFGVKHFEAAAGIVVTASHN 151 Query: 149 PPEYNGYKVYGDDGGQ-LPPKEADIVIEQVNAIENELTITVDEENKLKEKGLIKIIGEDI 207 PP+YNGYKVY ++G Q +PP +A I A EL + E ++G + + +D Sbjct: 152 PPKYNGYKVYWENGAQIIPPHDAGIAACIDRAANLELPWMPEPE--AVKQGRLSFLQDDF 209 Query: 208 DKVYTEK-LTSISVHP---ELSEEVDVKVVFTPLHGTANKPVRRGLEALGYKNVTVVKEQ 263 + Y L S +HP + + + +T +HG R L G+ V V Q Sbjct: 210 FERYRRAILHSPLLHPAGESQAGRASLGIAYTAMHGVGAPMAERVLRDAGFSQVYSVAAQ 269 Query: 264 ELPDSNFSTVTSPNPEEHAAFEYAIKLGEEQNADILIATDPDADRLGIAVKNDQGKYTVL 323 PD NF TV PNPEE A + I ++ A + A DPDADR +A + G Y +L Sbjct: 270 REPDGNFPTVNFPNPEEPGAMDMVIAEAGDKGALLACANDPDADRFALAARQSDGGYRML 329 Query: 324 TGNQTGALLLHYLLSEKKKQGILPDNGVVLKTIVTSEIGRAVASSFGLDTIDTLTGFKFI 383 +G+QTGALL YLLS + G+ +V TIV+S + A+A+ +G + TLTGFK++ Sbjct: 330 SGDQTGALLCDYLLSHWQGAGV----PLVGNTIVSSALLHAIAAHYGAHSYTTLTGFKWL 385 Query: 384 GEKIKEYEASGQYTFQFGYEESYGYLIGDFARDKDAIQAALLAVEVCAFYKKQGMSLYEA 443 ++ E + Q F F YEE+ GY +G+ DKD I A L + A +G ++ A Sbjct: 386 MNTAQQLE-TPQQPFLFAYEEALGYTVGNLVWDKDGISAQLCFANLAAELLAEGKDVWAA 444 Query: 444 LINLFNEYGFYREGLKSLTLKGKQGAEQIEAILASFRQNPPQKMAGKQVVTAEDYAVSKR 503 L L+ +G Y S+ L +G I A L R NPP ++ + VV ED R Sbjct: 445 LERLYRRHGLYVNRQVSIAL--GEGTPDIGAWL---RDNPPTEIDKRPVVAREDLK-RLR 498 Query: 504 TLLTESKEEAIDLPKSNVLKYFL-----EDGSW--FCLRPSGTEPKVKFYFAVKGSSLED 556 + + +EE I LP S+VL Y L GS +RPSGTEPK+K Y+ + +D Sbjct: 499 KVYADGREEEIALPASDVLIYHLGASDATPGSTARVIVRPSGTEPKIKCYYELVLPMADD 558 Query: 557 SEKRLAVLSEDVMKT 571 A L D + T Sbjct: 559 IAMADAQLQGDALMT 573 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: 766 Number of extensions: 35 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: 585 Length adjustment: 36 Effective length of query: 545 Effective length of database: 549 Effective search space: 299205 Effective search space used: 299205 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