Align phosphomannose mutase (EC 5.4.2.8) (characterized)
to candidate WP_002918370.1 KVAR_RS02555 phosphoglucosamine mutase
Query= metacyc::MONOMER-13382 (455 letters) >NCBI__GCF_000025465.1:WP_002918370.1 Length = 445 Score = 207 bits (527), Expect = 6e-58 Identities = 148/446 (33%), Positives = 222/446 (49%), Gaps = 22/446 (4%) Query: 3 KLFGTFGVRG-IANEKITPEFAMKIGMAFGTLLKREGRKKPLVVVGRDTRVSGEMLKEAL 61 K FGT G+RG + + ITPEF +K+G A G +L R G +K +++G+DTR+SG ML+ AL Sbjct: 5 KYFGTDGIRGRVGDAPITPEFVLKLGWAAGKVLARHGSRK--IIIGKDTRISGYMLESAL 62 Query: 62 ISGLLSVGCDVIDVGIAPTPAVQWATKHFNADGGAVITASHNPPEYNGIKLLEPNGMGLK 121 +GL + G G PTPA+ + T+ F A+ G VI+ASHNP NGIK G L Sbjct: 63 EAGLAAAGLSASFTGPMPTPAIAYLTRAFRAEAGIVISASHNPFYDNGIKFFSIEGTKLP 122 Query: 122 KEREAIVEELFFKEDFDRAKWYEIGEVRR-EDIIKPYIEAIKSKVDVEAIKKRKPFVVVD 180 + E +E KE E+G+ R D YIE K E + VVVD Sbjct: 123 DDVEEAIEAEMEKE-LTCVDSAELGKASRIVDAAGRYIEFCKGTFPNE-LSLGTLKVVVD 180 Query: 181 TSNGAGSLTLPYLLRELGCKVITVNAQPDGYFPARNPEPNEENLKEFMEIVKALGADFGV 240 ++GA P + RELG +VI + +PDG N E +++ V A AD G+ Sbjct: 181 CAHGATYHIAPNVFRELGAQVIAMGCEPDGL--NINEEVGATDVRALQARVLAEKADLGI 238 Query: 241 AQDGDADRAVFIDENGRFIQGDKTFALVADAVLKE---KGGGLLVTTVATSNLLDDIAKK 297 A DGD DR + +D G + GD+ ++A L++ +GG V T+ ++ L+ K+ Sbjct: 239 AYDGDGDRVIMVDHEGNKVDGDQILYIIAREGLRQGQLRGGA--VGTLMSNMGLELALKQ 296 Query: 298 HGAKVMRTKVGDLIVARALYENNGTIGGEENGGVIFPEHVLGRDGAMTVAKVVEIFAKSG 357 G R KVGD V L E IG E +G VI + DG + +VV ++ Sbjct: 297 LGIPFARAKVGDRYVLEMLQEKGWRIGAENSGHVILLDKTTTGDGIVASLQVVAAMVRNH 356 Query: 358 KKFSELIDELPKYYQIKTK-RHVEGDRHAIVNKVAEMARERGYTVDTTDGAKIIFEDGWV 416 +L + + Q+ R EG + + N+ + T + + + G V Sbjct: 357 MSLHDLCSGMKMFPQLLVNVRFTEGSGNPLENEHVKAV--------TAEVEAALGKRGRV 408 Query: 417 LVRASGTEPIIRIFSEAKSKEKAQEY 442 L+R SGTEP+IR+ E + +++ E+ Sbjct: 409 LLRKSGTEPLIRVMVEGEHEDQVHEF 434 Lambda K H 0.317 0.138 0.391 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: 498 Number of extensions: 35 Number of successful extensions: 6 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: 455 Length of database: 445 Length adjustment: 33 Effective length of query: 422 Effective length of database: 412 Effective search space: 173864 Effective search space used: 173864 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