Align phosphomannomutase (EC 5.4.2.8) (characterized)
to candidate WP_014449815.1 LFE_RS08505 phosphomannomutase/phosphoglucomutase
Query= BRENDA::P26276 (463 letters) >NCBI__GCF_000284315.1:WP_014449815.1 Length = 473 Score = 400 bits (1029), Expect = e-116 Identities = 202/453 (44%), Positives = 283/453 (62%), Gaps = 8/453 (1%) Query: 9 LPASIFRAYDIRGVVGDTLTAETAYWIGRAIGSESLARGEPCVAVGRDGRLSGPELVKQL 68 LP+ IFR YDIRGV LT E IG A G L G +++GRD R+S ++K Sbjct: 5 LPSRIFREYDIRGVAETELTDEIIDAIGTAYGQMVLECGGKTISIGRDVRVSSERILKSF 64 Query: 69 IQGLVDCGCQVSDVGMVPTPVLYYAANVLEGKSGVMLTGSHNPPDYNGFKIVVAGETLAN 128 + + G + D+G+VPTP+LY++ L GVM+T SHNPP NG K+ + ET+ Sbjct: 65 SEAITRLGIHILDIGIVPTPLLYFSLFHLPVDGGVMITASHNPPQDNGLKLAIGQETIHG 124 Query: 129 EQIQALRERIEKNDLASGV---GSVEQVDILPRYFKQIRDDIA-----MAKPMKVVVDCG 180 +I +RERIE+ V G + V + Y +IR+ + M +P++ V+DCG Sbjct: 125 SRIMEIRERIERPSAPPSVEKKGLIRPVPVRNSYISEIRERTSPLPAFMGRPIRAVIDCG 184 Query: 181 NGVAGVIAPQLIEALGCSVIPLYCEVDGNFPNHHPDPGKPENLKDLIAKVKAENADLGLA 240 NG G++A L ALG L+ DGNFPNHHPDP PENL+ LIA+V + AD+G+A Sbjct: 185 NGTGGLVARDLYNALGVRTELLFERPDGNFPNHHPDPSVPENLETLIAEVIKQKADIGIA 244 Query: 241 FDGDGDRVGVVTNTGTIIYPDRLLMLFAKDVVSRNPGADIIFDVKCTRRLIALISGYGGR 300 FDGD DR+GVVT G I+Y D+L++LF++ V+ RNPGA II +VK ++ L I+ GG+ Sbjct: 245 FDGDSDRIGVVTGKGEILYGDQLMVLFSEQVLKRNPGAMIISEVKASKVLYDEIARMGGK 304 Query: 301 PVMWKTGHSLIKKKMKETGALLAGEMSGHVFFKERWFGFDDGIYSAARLLEILSQDQRDS 360 P+MWK GHS+IK KMKE GA LAGEMSGH+FFK+ +FGFDD +Y+ R+L+ + + Q+ Sbjct: 305 PLMWKAGHSVIKAKMKEEGAPLAGEMSGHIFFKDGYFGFDDALYAGVRILQFMVEKQKSL 364 Query: 361 EHVFSAFPSDISTPEINITVTEDSKFAIIEALQRDAQWGEGNITTLDGVRVDYPKGWGLV 420 + S P +TPE+ + + KF +++ L+ + + +DGVRV+YP GWGLV Sbjct: 365 SELLSGIPKTANTPELRMDCPDALKFKLVDTLKSLLRDSGSSFVDIDGVRVEYPDGWGLV 424 Query: 421 RASNTTPVLVLRFEADTEEELERIKTVFRNQLK 453 RASNT P LVLRFE T E + I+ + L+ Sbjct: 425 RASNTQPALVLRFEGPTVERRDEIRNNIESMLQ 457 Lambda K H 0.319 0.138 0.410 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: 586 Number of extensions: 28 Number of successful extensions: 2 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: 473 Length adjustment: 33 Effective length of query: 430 Effective length of database: 440 Effective search space: 189200 Effective search space used: 189200 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 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