Align Phosphoglucomutase-1; PGM 1; Glucose phosphomutase 1; EC 5.4.2.2 (characterized)
to candidate WP_093428782.1 BM272_RS10670 alpha-D-glucose phosphate-specific phosphoglucomutase
Query= SwissProt::P38652 (562 letters) >NCBI__GCF_900112605.1:WP_093428782.1 Length = 543 Score = 580 bits (1496), Expect = e-170 Identities = 301/560 (53%), Positives = 398/560 (71%), Gaps = 20/560 (3%) Query: 4 IVTVKTQAYPDQKPGTSGLRKRVKVFQGNANYAENFIQSIVSTVEPALRQEATLVVGGDG 63 I TV TQ + DQKPGTSGLRKRV FQ NY ENF+QSI+ E + TLV+GGDG Sbjct: 3 IQTVATQPFDDQKPGTSGLRKRVTRFQ-QPNYLENFVQSILDVGEGL--RGGTLVLGGDG 59 Query: 64 RFYMTEAIQLIVRIAAANGIGRLVIGQNGILSTPAVSCIIRKIKAIGGIILTASHNPGGP 123 R+Y AIQ I+R+AAA+G+GR+++G++G+LSTPAVS IIRK +A GGI+L+ASHNPGGP Sbjct: 60 RYYNETAIQTILRMAAAHGVGRVLVGRDGLLSTPAVSAIIRKRRADGGIVLSASHNPGGP 119 Query: 124 NGDFGIKFNISNGGPAPEAITDKIFQISKTIEEYAICPDLKVDLGVLGKQQFDLENKFKP 183 GDFGIKFN +NGGPAPE++T+ I+Q S+T++EY I +DL G + + Sbjct: 120 EGDFGIKFNTANGGPAPESVTEAIYQRSRTLDEYRITDTGDIDLSREGAVEI------QG 173 Query: 184 FTVEIVDSVEAYATMLRNIFDFNALKELLSGPNRLKIRIDAMHGVVGPYVKKILCEELGA 243 TVE++D V YA ++ +FD A+ +++ RL R DAMH + GPY ++IL E LGA Sbjct: 174 TTVEVIDPVADYAALMEELFDMEAIAAMIADGFRL--RFDAMHAITGPYARRILEERLGA 231 Query: 244 PANSAVNCVPLEDFGGHHPDPNLTYAADLVETMKSGEH-DFGAAFDGDGDRNMILGKHGF 302 PA S +N PL DFGG HPDPNL +A +LV M + D GAA DGDGDRNMILG F Sbjct: 232 PAGSVINAEPLPDFGGGHPDPNLVHAPELVALMYGPDAPDLGAASDGDGDRNMILGPD-F 290 Query: 303 FVNPSDSVAVIAANIFSIPYFQQTGVRGFARSMPTSGALDRVANATKIASYETPTGWKFF 362 FV PSDS+A +AAN P + G+RG ARSMPTS A DRVA A + YETPTGWKFF Sbjct: 291 FVTPSDSLAFLAANATCAPGYAG-GIRGIARSMPTSAAADRVAEALGVPCYETPTGWKFF 349 Query: 363 GNLMDASKLSLCGEESFGTGSDHIREKDGLWAVLAWLSILATRKQRVEDILKDHWQKFGR 422 GNL+DA +++LCGEESFGTGS H+REKDGLWAVL WL+ILA R++ V D+L+DHWQ+FGR Sbjct: 350 GNLLDADRVTLCGEESFGTGSAHVREKDGLWAVLFWLNILAVRQRGVGDLLRDHWQRFGR 409 Query: 423 NFFTRYDYEEVEAEGANKMMKDLEALMLDRSFVGKQFSANDKVYTVEKADNFEYSDPVDG 482 N ++RYDYE V+AE A +M++ L + D G+ F+ TV AD+F Y+DP+DG Sbjct: 410 NVYSRYDYEGVDAEAAGRMVEGLRGRLAD--LPGQSFNG----LTVTAADDFAYTDPIDG 463 Query: 483 SISKNQGLRLIFADGSRIIFRLSGTGSAGATIRLYIDSYEKDAAKINQDPQVMLAPLISI 542 S +++QGLR+ F G R++FRLSGTG+ GAT+R+Y++++E + + ++ +LAPL + Sbjct: 464 SRAEHQGLRIFFQGGERLVFRLSGTGTEGATLRVYLEAFEGNPERQDRPTAELLAPLTAA 523 Query: 543 ALKVSQLQERTGRTAPTVIT 562 A ++ ++ TGR P VIT Sbjct: 524 AEALAGIRSHTGRAEPDVIT 543 Lambda K H 0.319 0.137 0.397 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: 866 Number of extensions: 52 Number of successful extensions: 10 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: 562 Length of database: 543 Length adjustment: 36 Effective length of query: 526 Effective length of database: 507 Effective search space: 266682 Effective search space used: 266682 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: 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