Align Phosphoglucosamine/phosphogalactosamine mutase; PGlcNM; EC 5.4.2.10; EC 5.4.2.13 (characterized)
to candidate WP_013451501.1 CALNI_RS06965 phosphomannomutase/phosphoglucomutase
Query= SwissProt::Q976E4 (455 letters) >NCBI__GCF_000183405.1:WP_013451501.1 Length = 473 Score = 154 bits (390), Expect = 5e-42 Identities = 141/482 (29%), Positives = 214/482 (44%), Gaps = 48/482 (9%) Query: 3 KLFGTDGVRGIVNKELTPELVLKLSKAIGTFFGKNSK--------ILVGRDVRAGGDMLV 54 K+F +RG+V + PE++ K IG FG+N K + VGRDVR + L Sbjct: 5 KIFRQYDIRGVVPDQFNPEIL----KIIGNTFGQNLKKKLNKVPVVSVGRDVRLSSNDLF 60 Query: 55 KIVEGGLLSVGVEVYDGGMAPTPALQYAVKTLGYDGGVVITASHNPAPYNGIKV-VDKDG 113 K + GL G +V + G PTP ++ L D ++IT SHNP YNG+K + KD Sbjct: 61 KGLTAGLTDAGCDVINLGTTPTPVTYFSSFKLHTDAFMMITGSHNPPEYNGLKFGIGKDT 120 Query: 114 IEIRREKENEIEDLFFTERFNTIEWSSLTTEVK---REDRVISTYVNGILSHVDIEKIK- 169 + I DL+ + I L T+ + ++ +IS Y+ + K K Sbjct: 121 VH-----SEGITDLY----NDIINGQYLITDKRGNIKDYDIISDYIQFYEENFTELKQKI 171 Query: 170 --KKNYKVLIDPANSVGALSTPLVARALGCKIYTINGNLDPLFSARQPEPTF-DSLKETA 226 K KV+ID N +L P + LG + + D F P+PT ++L + Sbjct: 172 RTIKGVKVVIDAGNGAASLVAPKIFELLGVDVVKLYCEPDGRFPNHHPDPTVEENLDDAK 231 Query: 227 EVVKTLKVDLGVAHDGDADRAIFIDSEGRVQWGDRSGTLLSYWASVKNPKAIKKIVTAVS 286 EVVK K D VA DGDADR +D G + WGD L Y +K KI+ V Sbjct: 232 EVVKIDKADFAVAFDGDADRIGVLDESGNIIWGDI--LLYIYARELKERYEKPKIIADVK 289 Query: 287 SSSLVEEYLSKYNIQVDWTKVGSVDIAHKVADENALAGFEENGGFMYPPHQYVRDGAMSF 346 SS L+ + L + K G I K+ + A E +G + + D A+ Sbjct: 290 SSKLLFDMLDNIGAEGIMWKTGHSLIKQKLKETGAELAGEMSGHIFFKDRFFGFDDAIYA 349 Query: 347 AL-MLELLANENVSS-----AELFDRLPKYY---LVKTKVD----LKPGLMVEEIYKKIL 393 A+ LE + ++L LPK Y ++ + D K + EI+ + L Sbjct: 350 AVRFLEAYVENKLEGKIEKCSDLTKDLPKVYNTPEIRFECDDNKKFKIVEQLSEIFNEYL 409 Query: 394 EVYSTSSVKAITIDGVKIIGKDFWFLVRKSGTEPIIRIMAEAKDENVANNLVNELKKIVE 453 + I+IDGV++ + W L+R S T+P++ + EA++ NN KKI E Sbjct: 410 KNGKLGIKSIISIDGVRVNFDNGWGLIRASNTQPVLVMRFEAENIEAMNN----YKKIFE 465 Query: 454 GK 455 + Sbjct: 466 AE 467 Lambda K H 0.316 0.136 0.384 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: 523 Number of extensions: 31 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: 473 Length adjustment: 33 Effective length of query: 422 Effective length of database: 440 Effective search space: 185680 Effective search space used: 185680 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