Align Phosphomannomutase/phosphoglucomutase; PMM / PGM; EC 5.4.2.2; EC 5.4.2.8 (uncharacterized)
to candidate GFF2403 PGA1_c24340 phosphomannomutase/phosphoglucomutase AlgC
Query= curated2:Q88C93 (463 letters) >FitnessBrowser__Phaeo:GFF2403 Length = 498 Score = 224 bits (571), Expect = 5e-63 Identities = 152/452 (33%), Positives = 240/452 (53%), Gaps = 21/452 (4%) Query: 14 FRAYDIRGVVGKTLHAETAYWIGRAIGAQSLAQGEPQV-SVGRDGRLSGPMLVEQLIKGL 72 FR YD R + ++ +G +G Q +G P V +V D R + LI GL Sbjct: 26 FREYDARWKYPEEINLPGMTALGLGLGTQMHKRGIPPVIAVANDYRDYSVAIKHALIIGL 85 Query: 73 VDAGCNVSDVGLVPTPALYYAANVLAGKSGVMLTGSHNPSDYNGFKIVIAGDTLANEQIQ 132 + AG V D+G +P Y+A L + M+T SHNP+ + G K+ Sbjct: 86 MQAGIEVRDIGPALSPMAYFAQFHLDVPAVAMVTASHNPNGWTGVKMGFERPLTHGPDEM 145 Query: 133 ALLTRLKTNDLTLAQ--GRVEKVE-ILDRYFKQIVGDVKLAKKLKVVVDCGNGAAGVVAP 189 L + N +A+ G + V+ + + Y +VGD K+++ LKVV GNG A AP Sbjct: 146 GELRDIVLNGEGVARPGGSYQFVDGVKEAYLDDLVGDFKMSRPLKVVCATGNGTASAFAP 205 Query: 190 QLIEALGCEVIPLFCEVDGNFPNHHPDPGKPENLEDLIAKVKETGADIGLAFDGDGDRVG 249 +L E +G EV+ +D FP+++P+P E L D+ A VK +GAD+ L FDGDGDR G Sbjct: 206 ELFERMGVEVVDSHNALDYTFPHYNPNPEAMEMLHDMSASVKASGADMALGFDGDGDRCG 265 Query: 250 VVTNTGSIVYPDRLLMLFAQDVLSRNPGAEIIFDVKCTRRLT--PLIEQHGGRALMWKTG 307 VV + G ++ D++ ++ A+D+ P + + DVK T P ++ +G A WKTG Sbjct: 266 VVDDEGEEIFADKVGVIMARDLSKLYPNSTFVADVKSTGLFASDPELKANGVTADYWKTG 325 Query: 308 HSLIKKKMKQTGSLLAGEMSGHIFIKER-WYGFDDGIYSAARLLEILSKT-EQSAENLFA 365 HS +K+++K+ G+L E SGH F+ E G+D G+ A + +++ + ++S +L Sbjct: 326 HSHMKRRVKEIGALAGFEKSGHYFLAEPVGRGYDCGMRVAVEICKLMDRNPDKSMSDLRK 385 Query: 366 AFPNDISTPEINIDVTDEGKFSIID----ALQRDADWGEA-------NLTTIDGVRVDYA 414 A P +TP ++ D K+++++ L A+ GE + T++G RV Sbjct: 386 ALPKTWATPTMSPYCADTEKYTVLERLVAKLVAKAEAGETLADRPIKEVVTVNGARVILD 445 Query: 415 NG-WGLVRASNTTPVLVLRFE-ADSDAELQRI 444 NG WGLVRAS+ TP LV+ E ++S+AEL+ I Sbjct: 446 NGSWGLVRASSNTPNLVVVCESSESEAELREI 477 Lambda K H 0.319 0.138 0.406 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: 575 Number of extensions: 39 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: 463 Length of database: 498 Length adjustment: 34 Effective length of query: 429 Effective length of database: 464 Effective search space: 199056 Effective search space used: 199056 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 51 (24.3 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