Align Phosphoglucomutase-2; PGM 2; Glucose phosphomutase 2; Phosphodeoxyribomutase; Phosphoglucomutase-1; Phosphopentomutase; EC 5.4.2.2; EC 5.4.2.7 (characterized)
to candidate WP_011778861.1 MVAN_RS08095 phospho-sugar mutase
Query= SwissProt::Q7TSV4 (620 letters) >NCBI__GCF_000015305.1:WP_011778861.1 Length = 532 Score = 248 bits (633), Expect = 5e-70 Identities = 197/585 (33%), Positives = 278/585 (47%), Gaps = 76/585 (12%) Query: 29 QWLRWDQNPLTSESVKQLIAGGNKEELRKCFGARMEFGTAGLRAPMGAGISRMNDLTIIQ 88 +WL D +P ++ +AG +++EL + F + FGTAGLR P+ AG + MN +++ Sbjct: 11 EWLSHDPDPASAAE----LAGCSEDELAERFAQPLTFGTAGLRGPLRAGPNGMNLAVVLR 66 Query: 89 TTQGFCRYLEKQFSDLKQRGVVISFDARAHPASGGSSRRFARLAATAFITQGVPVYLFSD 148 T R L + L VV+ +DAR A F R AA F QG V L Sbjct: 67 ATWAVARVLTDR--GLGGSQVVVGYDARHRSAE------FGRAAAEVFAAQGFSVTLMFA 118 Query: 149 ITPTPFVPYTVSHLKLCAGIMITASHNPKQDNGYKVYWDNGAQIISPHDRGISQAIEENL 208 PTP V + V AG+ ITASHNP QDNGYKVY+ G QI+SP DR I AI Sbjct: 119 AVPTPAVAFAVRGTGAAAGVQITASHNPPQDNGYKVYFPGGLQIVSPTDRDIEHAI---- 174 Query: 209 EPWPQAWEESLVDSSPLLHNPSASIGNDYFED-LKKYCFHRTVNKESKVKFVHTSVHGVG 267 S + + +P + G D L++ R +++ T +HGVG Sbjct: 175 --------ASAPPADEIPRSPVTASGEDQVRAYLERAASVRRTTGPARIAL--TPMHGVG 224 Query: 268 HEFV--QLAFKAFDLAPPEAVPQQKDPDPEFPTVKYPNPEEGKGVLTLSFALADKIKAKI 325 EF LA FD V +Q PDP+FPTV +PNPEE G L ALA + A I Sbjct: 225 GEFALDALALAGFD--DVHVVQRQFAPDPDFPTVAFPNPEE-PGASDLLLALAADVDADI 281 Query: 326 VLANDPDADRLAVAEKQDSGEWRVFSGNELGALLGWWLFTSWKEKNQDQSNLKDTYMLSS 385 +A DPDADR A+ +G WR+ SG+E G LLG ++ + ++K + S+ Sbjct: 282 AIALDPDADRCAIGVPTPAG-WRMLSGDETGWLLGDYILSDRQDK---------AVVAST 331 Query: 386 TVSSKILRAIALKEGFHFEETLTGFKWMGNRAQQLGDQGKTVLFAFEEAIGYMCCP-FVL 444 VSS++L +IA G ETLTGFKW+ + L + +++A+EEAIG+ P V Sbjct: 332 VVSSRMLASIAAAHGARHVETLTGFKWLARADEGLDAR---LVYAYEEAIGHCVDPDAVR 388 Query: 445 DKDGVSAAVICAELASFLATKNLSLSQQLNAIYVEYGYHITTASYFICHDQGTIQNLFGN 504 DKDG+SAAV+ +L L + ++ L+ + +G H TTA Sbjct: 389 DKDGISAAVLACDLVVALRGRGRTVPDALDDLARRHGVHTTTAV---------------- 432 Query: 505 LRNYDGKNNYPKMCGKFEIS---AIRDLTTGYDDSQPDKKAVLPTSKSSQMITFTFANGG 561 R D + M + + I + D QP A++ T A Sbjct: 433 TRRVDSPQDAAAMMTRLRAAPPDTIAGVAVTVADLQPRTDALVFTGGDD-------AASV 485 Query: 562 VATMRTSGTEPKIKYYAEL-CA---PPGNSDPEHLKKELDELVGA 602 +R SGTEPK+K Y E+ CA PG + L++ + V A Sbjct: 486 RVVIRPSGTEPKLKSYIEVRCAGELAPGRARAAALQEAVAAAVRA 530 Lambda K H 0.317 0.133 0.403 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: 804 Number of extensions: 38 Number of successful extensions: 8 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 620 Length of database: 532 Length adjustment: 36 Effective length of query: 584 Effective length of database: 496 Effective search space: 289664 Effective search space used: 289664 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 (21.6 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