Align Phosphoglucomutase-2; PGM 2; Glucose phosphomutase 2; Phosphodeoxyribomutase; Phosphopentomutase; EC 5.4.2.2; EC 5.4.2.7 (characterized)
to candidate 351076 BT1548 phosphoglucomutase phosphomannomutase (NCBI ptt file)
Query= SwissProt::Q96G03 (612 letters) >FitnessBrowser__Btheta:351076 Length = 581 Score = 312 bits (799), Expect = 3e-89 Identities = 194/566 (34%), Positives = 298/566 (52%), Gaps = 30/566 (5%) Query: 14 RLDQETAQWLRWDKNSLTLEAVKRLIAEGNKEELRKCFGARMEFGTAGLRAAMGPGISRM 73 ++ ++ +WL ++ T VKR++ +K EL + F +EFGT GLR MG G +RM Sbjct: 9 QVTEKAEKWLTPAYDAETQAEVKRMLENEDKTELIEAFYKDLEFGTGGLRGIMGVGSNRM 68 Query: 74 NDLTIIQTTQGFCRYLEKQFSDLKQKGIVISFDARAHPSSGGSSRRFARLAATTFISQGI 133 N T+ TQG YL+K F DL Q +V+ D R +SR FA +A F + GI Sbjct: 69 NIYTVGAATQGLSNYLKKNFKDLPQISVVVGHDCR------NNSRLFAETSANIFSANGI 122 Query: 134 PVYLFSDITPTPFVPFTVSHLKLCAGIMITASHNPKQDNGYKVYWDNGAQIISPHDKGIS 193 VYLF D+ PTP + F + HL +GI++TASHNPK+ NGYK YWD+GAQ+++PHD GI Sbjct: 123 KVYLFDDMRPTPEMSFAIRHLGCQSGIILTASHNPKEYNGYKAYWDDGAQVLAPHDAGII 182 Query: 194 QAIEENLEPWPQAWDDSLIDSSPLLHNPSASINNDYFEDLKKYCFH-RSVNRETKVKFVH 252 + A D + L+ I+ Y + +K ++ R +K V+ Sbjct: 183 DEVNN----IASAADIKFKGNPDLIQIIGEDIDKIYLDMVKTVSIDPEAIARHKDMKIVY 238 Query: 253 TSVHGVGHSFVQSAFKAFDLVPPEAVPEQKDPDPEFPTVKYPNPEEGKGVLTLSFALADK 312 T +HG G + A K + VPEQ D FPTV PNPE + L+++ LA + Sbjct: 239 TPIHGTGMMLIPRALKMWGFENVFTVPEQMIKDGNFPTVISPNPENAE-ALSMAVNLAKE 297 Query: 313 TKARIVLANDPDADRLAVAEKQDSGEWRVFSGNELGALLGWWLFTSWKEKNQDRSALKDT 372 A +V+A+DPDADR+ +A K D GEW + +GN+ + +++ T +K+ + + + Sbjct: 298 IDADLVMASDPDADRVGIACKDDKGEWVLINGNQTCMMYLYYILTQYKQLGKIKG---NE 354 Query: 373 YMLSSTVSSKILRAIALKEGFHFEETLTGFKWMGNRAKQLIDQGKTVLFAFEEAIGYMCC 432 + + + V++++++ IA K + TGFKW+ R +L + K + EE+ G++ Sbjct: 355 FCVKTIVTTELIKKIADKNNIEMLDCYTGFKWIA-REIRLREGKKKYIGGGEESYGFLAE 413 Query: 433 PFVLDKDGVSAAVISAELASFLATKNLSLSQQLKAIYVEYGY------HITKASYFICHD 486 FV DKD VSA + AE+A++ SL Q L IYVEYG+ ++ K Sbjct: 414 DFVRDKDAVSACCLIAEVAAWAKDNGKSLYQLLLDIYVEYGFSKEFTVNVVKPGK---SG 470 Query: 487 QETIKKLFENLRNYDGKNNYPKACGKFEISAIRDLTTGYDDSQPDKKAVLPTSKSSQMIT 546 E IK + EN R N PK G ++ +D T K L ++S ++ Sbjct: 471 AEEIKAMMENFR-----ANPPKELGGSKVILSKDYKTLKQTDAEGKVTDLDMPETSNVLQ 525 Query: 547 FTFANGGVATMRTSGTEPKIKYYAEL 572 + +G ++R SGTEPKIK+Y E+ Sbjct: 526 YFTEDGSKVSVRPSGTEPKIKFYMEV 551 Lambda K H 0.317 0.133 0.399 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: 881 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: 612 Length of database: 581 Length adjustment: 37 Effective length of query: 575 Effective length of database: 544 Effective search space: 312800 Effective search space used: 312800 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 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