Align phosphomannose mutase (EC 5.4.2.8) (characterized)
to candidate WP_022949929.1 H035_RS0115785 phosphoglucosamine mutase
Query= metacyc::MONOMER-13382 (455 letters) >NCBI__GCF_000421465.1:WP_022949929.1 Length = 446 Score = 191 bits (484), Expect = 5e-53 Identities = 138/442 (31%), Positives = 216/442 (48%), Gaps = 16/442 (3%) Query: 3 KLFGTFGVRGIANEK-ITPEFAMKIGMAFGTLLKREGRKKPLVVVGRDTRVSGEMLKEAL 61 + FGT G+RG E ITP+F +K+G A G + + G V+VG+DTR+SG M + AL Sbjct: 4 RYFGTDGIRGKVGEAPITPDFVLKLGWAAGQVFRDNGSSH--VLVGKDTRISGYMFESAL 61 Query: 62 ISGLLSVGCDVIDVGIAPTPAVQWATKHFNADGGAVITASHNPPEYNGIKLLEPNGMGLK 121 +GL + G D +G PTP + + T+ A G VI+ASHNP NGIK G L Sbjct: 62 EAGLSAAGVDTQLLGPMPTPGIAYLTRTLRAKAGIVISASHNPYTDNGIKFFSGAGKKLP 121 Query: 122 KEREAIVEELFFKEDFDRAKWYEIGE-VRREDIIKPYIEAIKSKVDVEAIKKRKPFVVVD 180 E EA + E ++ +G+ +R D YIE KS V + +V+D Sbjct: 122 DEIEAAI-ETHLEQPMTTVASDRLGKALRIGDAAGRYIEFCKSTVP-SCMDLSGLHLVLD 179 Query: 181 TSNGAGSLTLPYLLRELGCKVITVNAQPDGYFPARNPEPNEENLKEFMEIVKALGADFGV 240 ++GA P++ E+G +V + QP+G N + + + V A GAD G+ Sbjct: 180 CAHGATYHIAPHVFTEVGARVDCIGTQPNGL--NINQDCGSIHAQALQREVVARGADLGI 237 Query: 241 AQDGDADRAVFIDENGRFIQGDKTFALVADAVL-KEKGGGLLVTTVATSNLLDDIAKKHG 299 A DGD DR + +D G + GD+ ++A + L K G +V T+ T+ L+ + G Sbjct: 238 AFDGDGDRVLMVDHTGALVDGDELLYIIAASRLGAGKLEGPVVGTLMTNLGLEHALAELG 297 Query: 300 AKVMRTKVGDLIVARALYENNGTIGGEENGGVIFPEHVLGRDGAMTVAKVVEIFAKSGKK 359 ++R +VGD V L + G +GGE +G +I + DG ++ +V+ +SGK Sbjct: 298 VDLLRAQVGDRYVMEMLETHGGILGGEGSGHIICLDRTTTGDGIVSALQVLAEMWRSGKS 357 Query: 360 FSELIDELPKYYQIKTKRHVEGDRHAIVNKVAEMARERGYTVDTTDGAKIIFEDGWVLVR 419 ++L + KY Q+ V+ + + G + + G VL+R Sbjct: 358 LAQLRQGMRKYPQVLHNVRVKAKPPRLDTVAPVWTAKEGV-------ERKLQGSGRVLLR 410 Query: 420 ASGTEPIIRIFSEAKSKEKAQE 441 SGTEP+IR+ E + + E Sbjct: 411 PSGTEPVIRVMIEGRDADLIDE 432 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: 501 Number of extensions: 24 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: 446 Length adjustment: 33 Effective length of query: 422 Effective length of database: 413 Effective search space: 174286 Effective search space used: 174286 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