Align phosphomannose mutase (EC 5.4.2.8) (characterized)
to candidate WP_019612989.1 G327_RS0101490 phosphoglucosamine mutase
Query= metacyc::MONOMER-13382 (455 letters) >NCBI__GCF_000381745.1:WP_019612989.1 Length = 443 Score = 204 bits (519), Expect = 5e-57 Identities = 155/447 (34%), Positives = 225/447 (50%), Gaps = 33/447 (7%) Query: 3 KLFGTFGVRG-IANEKITPEFAMKIGMAFGTLLKREGRKKPLVVVGRDTRVSGEMLKEAL 61 K FGT G+RG + ITPEFA+K+G A G +L + G KK V++G+D R+SG ML+ AL Sbjct: 4 KYFGTDGIRGKVGASLITPEFALKLGWAAGRVLAKSGSKK--VLIGKDPRISGYMLEAAL 61 Query: 62 ISGLLSVGCDVIDVGIAPTPAVQWATKHFNADGGAVITASHNPPEYNGIKLLEPNGMGLK 121 +GL + G + +G PTPAV + T F A G VI+ASHNP NGIK G L Sbjct: 62 QAGLTAAGLRPVLMGPMPTPAVAYLTHTFRATAGIVISASHNPYYDNGIKFFSDKGTKLS 121 Query: 122 KEREAIVEELFFKEDFDRAKWYEIGEVRR-EDIIKPYIEAIKS----KVDVEAIKKRKPF 176 ++ E +E KE ++G+ R ED YIE KS K D+ +K Sbjct: 122 EKVELEIEAEIDKE-LKCVDSSQLGKAYRIEDAAGRYIEFCKSTFPTKYDLSGLK----- 175 Query: 177 VVVDTSNGAGSLTLPYLLRELGCKVITVNAQPDGYFPARNPEPNEENLKEFMEIVKALGA 236 +VVD +NGA P ++ ELG KVI++ +P+G N +++ E V A Sbjct: 176 IVVDCANGATYHIAPLVINELGAKVISMGVEPNGV--NINLNCGATSMQALSERVVKEKA 233 Query: 237 DFGVAQDGDADRAVFIDENGRFIQGDKTFALVADAVLKE---KGGGLLVTTVATSNLLDD 293 D+G+A DGD DR + +D G + GD+ ++A L+ KGG V T ++ L+ Sbjct: 234 DYGIAFDGDGDRVMMVDHTGYILDGDELLYIIARDKLRTGTLKGGA--VGTKMSNLGLEQ 291 Query: 294 IAKKHGAKVMRTKVGDLIVARALYENNGTIGGEENGGVIFPEHVLGRDGAMTVAKVVEIF 353 K G R+ VGD V + +NN IG E +G VI + + DG ++ +V+ Sbjct: 292 ALKTLGIPFERSDVGDRHVMELMNKNNWCIGAENSGHVICSDLLPTGDGIVSGLQVMSAM 351 Query: 354 AKSGKKFSELIDELPKYYQIKTKRHVEGDRHAIVNK--VAEMARERGYTVDTTDGAKIIF 411 S EL + KY Q+ + + +K +AE R ++ Sbjct: 352 QGSRMTLHELRQGMKKYPQVLLNVRFNNEIDPLQDKDILAEQKRIE----------DLLG 401 Query: 412 EDGWVLVRASGTEPIIRIFSEAKSKEK 438 E G VL+R SGTEP+ R+ EA KE+ Sbjct: 402 ERGRVLLRKSGTEPVFRVMVEADDKEE 428 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: 511 Number of extensions: 29 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: 443 Length adjustment: 33 Effective length of query: 422 Effective length of database: 410 Effective search space: 173020 Effective search space used: 173020 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