Align phosphomannomutase (EC 5.4.2.8) (characterized)
to candidate WP_093428362.1 BM272_RS08525 phosphomannomutase/phosphoglucomutase
Query= BRENDA::P26276 (463 letters) >NCBI__GCF_900112605.1:WP_093428362.1 Length = 473 Score = 420 bits (1080), Expect = e-122 Identities = 219/461 (47%), Positives = 299/461 (64%), Gaps = 4/461 (0%) Query: 1 MSTAKAPTLPAS-IFRAYDIRGVVGDTLTAETAYWIGRAIGSESLARGEPCVAVGRDGRL 59 M+ A LPA+ +FR YDIRG D + A+W+GRAI + + VA+GRDGRL Sbjct: 1 MTVAGPEHLPAAELFRTYDIRGAAADLAEGDAAWWLGRAIATVAAESAPGPVALGRDGRL 60 Query: 60 SGPELVKQLIQGLVDCGCQVSDVGMVPTPVLYYAANVLEGKSGVMLTGSHNPPDYNGFKI 119 S P + + GL G V D+G +PTP+LYY A L +GVM+T SHNPP NG KI Sbjct: 61 SSPAIAAAVADGLRAGGANVIDLGAIPTPLLYYGAWRLARGNGVMVTASHNPPADNGLKI 120 Query: 120 VVAGETLANEQIQALRERIEKNDLASGVGSVEQVDILPRYFKQIRDDIAMAKPMKVVVDC 179 V+ TL + I+ LR R+++ L G GS DIL Y +I +DI + +P++VVVD Sbjct: 121 VLGRRTLFGDGIRDLRHRLQEGALTRGDGSYRTADILADYRSRIAEDIRLERPLEVVVDA 180 Query: 180 GNGVAGVIAPQLIEALGCSVIPLYCEVDGNFPNHHPDPGKPENLKDLIAKVKAENADLGL 239 GNG+AG A ++EALG V PL+CE DG+FP+HHPDP +PENL DL V+ + ADLGL Sbjct: 181 GNGIAGPAAVAVLEALGARVHPLHCEPDGHFPHHHPDPSRPENLADLAEAVRHQGADLGL 240 Query: 240 AFDGDGDRVGVVTNTGTIIYPDRLLMLFAKDVVSRNPGADIIFDVKCTRRLIALISGYGG 299 AFDGDGDR+GVV G +++PDRLL LF +V++ PGA ++FDVK T L + I+ GG Sbjct: 241 AFDGDGDRLGVVDEQGRMVWPDRLLALFLPEVLAARPGAAVLFDVKSTGALFSAITEAGG 300 Query: 300 RPVMWKTGHSLIKKKMKETGALLAGEMSGHVFFKERWFGFDDGIYSAARLLEILSQDQRD 359 RPVM +GHSLI+ +M+ GA+LAGE++GH+F +RWFGFDD +Y+AAR+LE++++ Sbjct: 301 RPVMTPSGHSLIRARMEAEGAVLAGELTGHLFLADRWFGFDDALYAAARILELVARAPTT 360 Query: 360 SEHVFSAFPSD-ISTPEINITVTEDSKFAIIEALQRDAQWGEGNITTLDGVRVDYPKGWG 418 ++ + P D ++TPEI++ V +I ALQ TT+DG+R+D+P+GWG Sbjct: 361 ADAL--GEPGDCVATPEIHLPVARAHGQTVIAALQAMTPPPGAAATTVDGLRLDFPRGWG 418 Query: 419 LVRASNTTPVLVLRFEADTEEELERIKTVFRNQLKAVDSSL 459 L+R SNT LVLRFEA EL + R L VD +L Sbjct: 419 LIRLSNTADALVLRFEAADVGELAAQREQLRRMLAEVDPAL 459 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: 587 Number of extensions: 22 Number of successful extensions: 3 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