Align phosphomannose mutase (EC 5.4.2.8) (characterized)
to candidate Ac3H11_444 Phosphoglucosamine mutase (EC 5.4.2.10)
Query= metacyc::MONOMER-13382 (455 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_444 Length = 444 Score = 212 bits (540), Expect = 2e-59 Identities = 147/439 (33%), Positives = 228/439 (51%), Gaps = 18/439 (4%) Query: 5 FGTFGVRG-IANEKITPEFAMKIGMAFGTLLKREGRKKPLVVVGRDTRVSGEMLKEALIS 63 FGT G+RG + ITP+F +++ A G +L R+ ++P V++G+DTR+SG ML+ AL S Sbjct: 6 FGTDGIRGTVGQPPITPDFVLRLAHAVGRVL-RQTEERPTVLIGKDTRISGYMLESALES 64 Query: 64 GLLSVGCDVIDVGIAPTPAVQWATKHFNADGGAVITASHNPPEYNGIKLLEPNGMGLKKE 123 G S G DV+ +G PTP V + T+ A G VI+ASHNP NGIK G L Sbjct: 65 GFNSAGVDVVLLGPLPTPGVAYLTRAQRASLGVVISASHNPYPDNGIKFFSAQGTKLSDA 124 Query: 124 REAIVEELFFKEDFDRAKWYEIGEVRR-EDIIKPYIEAIKSKVDVEAIKKRKPFVVVDTS 182 E VEE + A +G+ RR +D YIE KS + K +VVD + Sbjct: 125 WELAVEEALAQSPV-WADSASLGKARRLDDAAGRYIEFCKSTFPQDLTLKGLK-IVVDAA 182 Query: 183 NGAGSLTLPYLLRELGCKVITVNAQPDGYFPARNPEPNEENLKEFMEIVKALGADFGVAQ 242 +GA P + ELG +V+++ PDG N E + + V+A AD+G+A Sbjct: 183 HGAAYQVAPKVFHELGAEVLSIGCAPDGL--NINHEVGATHPDALVRAVRANRADYGIAL 240 Query: 243 DGDADRAVFIDENGRFIQGDKTFALVA-DAVLKEKGGGLLVTTVATSNLLDDIAKKHGAK 301 DGDADR +D GR GD+ L+A D + +++ +V T+ T+ ++ + G K Sbjct: 241 DGDADRLQVVDATGRLYNGDELLYLMASDRMGRDEHVPGVVGTLMTNMAVEVALQSRGVK 300 Query: 302 VMRTKVGDLIVARALYENNGTIGGEENGGVIFPEHVLGRDGAMTVAKVVEIFAKSGKKFS 361 +R KVGD V L + +GGE +G ++ + DG ++ +V++ +SG+ + Sbjct: 301 FVRAKVGDRYVLEELARHRWLLGGEGSGHLLALDRHTTGDGLVSALQVLQACVRSGQTLA 360 Query: 362 ELIDELPKYYQIKTKRHVEGDRHAIVNKVAEMARERGYTVDTTDGA-KIIFEDGWVLVRA 420 +L+ E+ Y Q+ + + N++ DTT + + G VL+RA Sbjct: 361 QLLAEVTLYPQVLLNVRLAPGQDWKSNRL---------LADTTQAVERDLGASGRVLIRA 411 Query: 421 SGTEPIIRIFSEAKSKEKA 439 SGTEP++R+ EA+ E A Sbjct: 412 SGTEPLLRVMVEARDAEMA 430 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: 445 Number of extensions: 23 Number of successful extensions: 5 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: 444 Length adjustment: 33 Effective length of query: 422 Effective length of database: 411 Effective search space: 173442 Effective search space used: 173442 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 17 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