Align phosphomannomutase (EC 5.4.2.8) (characterized)
to candidate WP_071387277.1 OLEAN_RS20470 phosphomannomutase/phosphoglucomutase
Query= BRENDA::P26276 (463 letters) >NCBI__GCF_000967895.1:WP_071387277.1 Length = 831 Score = 459 bits (1180), Expect = e-133 Identities = 222/453 (49%), Positives = 309/453 (68%), Gaps = 1/453 (0%) Query: 12 SIFRAYDIRGVVGDTLTAETAYWIGRAIGSESLARGEPCVAVGRDGRLSGPELVKQLIQG 71 SIFRAYDIRG V D LT + A IG A+GSE L RGE + +G DGRLS PEL L +G Sbjct: 379 SIFRAYDIRGTVNDNLTPDVAEQIGLALGSELLIRGESKIVLGWDGRLSSPELAAALQKG 438 Query: 72 LVDCGCQVSDVGMVPTPVLYYAANVLEGKSGVMLTGSHNPPDYNGFKIVVAGETLANEQI 131 L+ GC V ++G V T ++YYA + L+ +G+++TGSHN NGFKI++ +TL E + Sbjct: 439 LLSTGCNVINIGSVVTGMMYYACHELDTTNGIIVTGSHNDSSLNGFKIIINRQTLIKESL 498 Query: 132 QALRERIEKNDLASGVGSVEQVDILPRYFKQIRDDIAMAKPMKVVVDCGNGVAGVIAPQL 191 AL RI++ D +G G +E+ +I Y +I+ DI +++P+KVV D GNG+AG I +L Sbjct: 499 MALYHRIQRKDFRTGQGLIEEKNISHDYLDRIQSDIQLSRPLKVVFDAGNGIAGPIGLKL 558 Query: 192 IEALGCSVIPLYCEVDGNFPNHHPDPGKPENLKDLIAKVKAENADLGLAFDGDGDRVGVV 251 ++ +G V+PL+C VDGNFPNH P+P P++L L V + ADLG+A DGDGD +G+V Sbjct: 559 LKTMGLEVVPLFCNVDGNFPNHKPNPSDPKSLIALQQAVVEQGADLGIAVDGDGDSIGLV 618 Query: 252 TNTGTIIYPDRLLMLFAKDVVSRNPGADIIFDVKCTRRLIALISGYGGRPVMWKTGHSLI 311 G+II PDR+LML AKD++SR+PG D+I+D+K +RRL +I+ GGRP MWKTG SL+ Sbjct: 619 DEKGSIIMPDRILMLLAKDIISRHPGCDVIYDIKSSRRLNQVIAQCGGRPTMWKTGQSLM 678 Query: 312 KKKMKETGALLAGEMSGHVFFKERWFGFDDGIYSAARLLEILSQDQRDSEHVFSAFPSDI 371 K KM+E A L GE+SGH++F++RW+GFDD +Y +ARLLE+LS +FS FP D+ Sbjct: 679 KAKMEELQATLGGELSGHIYFRDRWYGFDDSLYVSARLLELLSHQLDTVSEIFSEFPDDV 738 Query: 372 STPEINITVTEDSKFAIIEALQRDAQWGEG-NITTLDGVRVDYPKGWGLVRASNTTPVLV 430 ST EI I SKF II+ L + +G ++T+DG+R D+ GWGL+RASNT+P L Sbjct: 739 STDEITINTDNKSKFDIIQKLASEPSLQQGARVSTIDGIRSDFQDGWGLIRASNTSPKLT 798 Query: 431 LRFEADTEEELERIKTVFRNQLKAVDSSLPVPF 463 LRF D + L RI+ ++++ L L +PF Sbjct: 799 LRFAGDNNDALLRIQLLYKDALLRHAPGLNIPF 831 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: 794 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: 831 Length adjustment: 37 Effective length of query: 426 Effective length of database: 794 Effective search space: 338244 Effective search space used: 338244 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