Align Phosphoglucomutase-2; PGM 2; Glucose phosphomutase 2; Phosphodeoxyribomutase; Phosphopentomutase; EC 5.4.2.2; EC 5.4.2.7 (characterized)
to candidate WP_013444375.1 PALPR_RS04220 phospho-sugar mutase
Query= SwissProt::Q96G03 (612 letters) >NCBI__GCF_000183135.1:WP_013444375.1 Length = 582 Score = 323 bits (827), Expect = 2e-92 Identities = 196/579 (33%), Positives = 314/579 (54%), Gaps = 24/579 (4%) Query: 22 WLRWDKNSLTLEAVKRLIAEGNKEELRKCFGARMEFGTAGLRAAMGPGISRMNDLTIIQT 81 WL + N T + V+RL+ +K EL + F +EFGT GLR MG G +RMN T+ Sbjct: 17 WLDGNYNEETKKEVRRLLEAEDKSELIESFYRDLEFGTGGLRGIMGVGTNRMNIYTVGAA 76 Query: 82 TQGFCRYLEKQFSDLKQKGIVISFDARAHPSSGGSSRRFARLAATTFISQGIPVYLFSDI 141 TQG YL+ QF D+ Q +VI D R +SR F+ ++A F + GI VYLF D+ Sbjct: 77 TQGLSNYLKAQFPDVPQLSVVIGHDCR------NNSRLFSEISANIFSANGIKVYLFEDL 130 Query: 142 TPTPFVPFTVSHLKLCAGIMITASHNPKQDNGYKVYWDNGAQIISPHDKGISQAIEENLE 201 PTP F + HL +GI++TASHNPK+ NGYK YW++GAQ+++PHD+ + + + Sbjct: 131 RPTPEASFAIRHLGCQSGIILTASHNPKEYNGYKAYWNDGAQMVAPHDENVITEVNK--- 187 Query: 202 PWPQAWDDSLIDSSP-LLHNPSASINNDYFEDLKKYCFH-RSVNRETKVKFVHTSVHGVG 259 + DD + +P L+ I+ + E++KK S+ R + +K V+T +HG G Sbjct: 188 --IASVDDIKFEGNPALIEIIGEEIDKLFIENIKKLSLSPESIKRNSNLKIVYTPIHGTG 245 Query: 260 HSFVQSAFKAFDLVPPEAVPEQKDPDPEFPTVKYPNPEEGKGVLTLSFALADKTKARIVL 319 + A K + AVPEQ FPTV PNPEE L ++ A +T A IV+ Sbjct: 246 VKLIPRALKEYGFTNIIAVPEQNVVSGNFPTVVSPNPEE-PAALDMAVKKAIETDADIVM 304 Query: 320 ANDPDADRLAVAEKQDSGEWRVFSGNELGALLGWWLFTSWKEKNQDRSALKDTYMLSSTV 379 A+DPDADRL +A K D GEW + +GN+ L ++L WKE + + Y++ + V Sbjct: 305 ASDPDADRLGIAVKNDKGEWILVNGNQTALLFIYYLIRRWKELGKLNG---NQYIVKTIV 361 Query: 380 SSKILRAIALKEGFHFEETLTGFKWMGNRAKQLIDQG-KTVLFAFEEAIGYMCCPFVLDK 438 +++I++ IA + G + TGFKW+ ++ ++G K + EE+ G++ F DK Sbjct: 362 TTEIIKQIAERNGVEMFDCFTGFKWIAAVIRE--NEGKKEYIGGGEESYGFLPEEFARDK 419 Query: 439 DGVSAAVISAELASFLATKNLSLSQQLKAIYVEYGYHITKASYFICHDQETIKKLFENLR 498 D VS+ + AE+A++ +L + L+ IYVEYGY K + + +++ + +R Sbjct: 420 DAVSSCTVMAEIAAWAKDNGKTLFELLQDIYVEYGYGKEKGISVVRKGKSGAEEIAQMMR 479 Query: 499 NYDGKNNYPKACGKFEISAIRDL-TTGYDDSQPDKKAVLPTSKSSQMITFTFANGGVATM 557 ++ ++N PK ++ ++D + D K + L +S ++ + +G ++ Sbjct: 480 DF--RSNPPKEIAGSKVKVVKDYDSLKMTDLDSGKVSDLIMPATSNVLQYFTEDGTKISV 537 Query: 558 RTSGTEPKIKYYAEL-CAPPGNSDPEQLKKELNELVSAI 595 R SGTEPKIK+Y E+ A +D + N+ + A+ Sbjct: 538 RPSGTEPKIKFYIEVRGAMTSRADYDAADAAANKKIEAV 576 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: 891 Number of extensions: 47 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: 582 Length adjustment: 37 Effective length of query: 575 Effective length of database: 545 Effective search space: 313375 Effective search space used: 313375 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 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