Align Phosphoglucomutase/phosphomannomutase; PGM/PMM; EC 5.4.2.2; EC 5.4.2.8 (characterized)
to candidate WP_013538031.1 THEAM_RS06450 phosphoglucomutase
Query= SwissProt::Q68BJ6 (456 letters) >NCBI__GCF_000185805.1:WP_013538031.1 Length = 461 Score = 235 bits (600), Expect = 2e-66 Identities = 155/463 (33%), Positives = 241/463 (52%), Gaps = 21/463 (4%) Query: 5 FGTFGVRGIANEEITPEFALKIGMAFGTLLKREGRERPLVVVGRDTRVSGEMLKDALISG 64 FGT G RG+ + E T + K+ +A G LLK +G +R VVVG D R E + Sbjct: 4 FGTDGWRGVISREFTFDNLRKVALAHGKLLKEQGAKR--VVVGYDLRFLSEEYGRFVAEI 61 Query: 65 LLSTGCD-VIDVGIAPTPAIQWATNHFNADGGAVITASHNPPEYNGIKLLEPNGMGLKKE 123 G + V+ G PTPA+ + T + N D G VITASHN +YNG K+ E G + E Sbjct: 62 FAGMGFETVLSDGFCPTPAVSYNTKYGNFDNGVVITASHNYGKYNGYKVKESFGGAARTE 121 Query: 124 REAIVEELFFSEDFHRAKWNEIGELRKEDIIKPYIEAIKNRVDVEAIKKRRPFVVVDTSN 183 +E+ + A GE + ED++ PY+E ++++++ K++ +V D Sbjct: 122 FTKEIEKRIPEVESLEAPK---GEPKLEDLVTPYVEGARSQIELSLFKEKSVKIVHDPMY 178 Query: 184 GAGSLTLPYLLRELGCKVVSVNAHPDGHFPARNPEPN-EENLKGFMEIVKALGADFGVAQ 242 GA L +V ++A+ D F ++PEP EEN+ ME V+AL AD G+A Sbjct: 179 GAQQGCFVKALVGTKAEVTEIHAYRDPLFGGKHPEPIVEENITALMEKVRALKADIGIAN 238 Query: 243 DGDADRAVFIDENGRFIQGDKTFALVADAVLRENGG--GLLVTTIATSNLLDDIAKRNGA 300 DGD DR ++E G F+ +AL+ ++R G G++V T++T L+D I ++ G Sbjct: 239 DGDGDRVGIVNEKGEFVNSQIVYALLLLHIIRNKGRREGVVVKTVSTGYLVDRICRKLGI 298 Query: 301 KVMRTKVGDLIVARALLENNGTIGGEENGGVIFPDFVLGRDGAMTTAKIVEIFAKSGKKF 360 +++ VG + +L GGEE+GG D++ RDG + +VE K Sbjct: 299 ELIEVPVGFKNITEVILRQKVLFGGEESGGYALVDYLPERDGLLMGLLMVEKMLAEEKSV 358 Query: 361 SELIDELPK-----YYQFKTKRHVEGDRKAIVAKVAELAEK-----KGYKIDTTDGTKII 410 S++++EL K YY+ E +RKA+ ++ E K K KI T DG KII Sbjct: 359 SQMVEELFKEFGAAYYKRMDLPVTEEERKAL-ERIKENPPKEWEGLKVSKILTIDGVKII 417 Query: 411 F-DDGWVLVRASGTEPIIRIFSEAKSEEKAREYLELGIKLLEE 452 F DD W+L R SGTEP+ R+++E ++ + L G+ L+++ Sbjct: 418 FEDDSWILFRPSGTEPVFRVYAETPEPKRTEKLLSWGVTLVKQ 460 Lambda K H 0.317 0.139 0.396 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: 546 Number of extensions: 37 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: 456 Length of database: 461 Length adjustment: 33 Effective length of query: 423 Effective length of database: 428 Effective search space: 181044 Effective search space used: 181044 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: 51 (24.3 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