Align phosphomannose mutase (EC 5.4.2.8) (characterized)
to candidate RR42_RS13475 RR42_RS13475 phosphoglucosamine mutase
Query= metacyc::MONOMER-13382 (455 letters) >FitnessBrowser__Cup4G11:RR42_RS13475 Length = 448 Score = 216 bits (551), Expect = 9e-61 Identities = 151/455 (33%), Positives = 236/455 (51%), Gaps = 37/455 (8%) Query: 3 KLFGTFGVRGIANEK-ITPEFAMKIGMAFGTLL----KREGRKKPLVVVGRDTRVSGEML 57 K FGT G+RG E ITP+F M++G A G +L K+ + +P V++G+DTR+SG ML Sbjct: 4 KYFGTDGIRGRVGEAPITPDFVMRLGYAAGMVLAHGAKQHDQARPTVLIGKDTRISGYML 63 Query: 58 KEALISGLLSVGCDVIDVGIAPTPAVQWATKHFNADGGAVITASHNPPEYNGIKLLEPNG 117 + AL +G S G +V+ G PTP V + T+ G VI+ASHNP NGIK +G Sbjct: 64 EAALEAGFTSAGVNVLLTGPLPTPGVAYLTRALRLSAGVVISASHNPYYDNGIKFFSADG 123 Query: 118 MGLKKEREAIVEELFFKEDFDRAKWYEIGEVRR-EDIIKPYIEAIKSKVDVEAIKKRKPF 176 L E +E+ +E + ++G RR ED YIE KS E K Sbjct: 124 DKLPDAVEMAIEQA-LEEPMVCVRSDDLGRARRIEDAAGRYIEFCKSTFPYEQ-DLHKLK 181 Query: 177 VVVDTSNGAGSLTLPYLLRELGCKVITVNAQPDGY-----FPARNPEPNEENLKEFMEIV 231 +VVD ++GA P++ ELG VI++ QPDG + A PE + +E V Sbjct: 182 LVVDCAHGAAYHIAPHVFHELGADVISIGNQPDGRNINAGYGATAPE-------KLIEAV 234 Query: 232 KALGADFGVAQDGDADRAVFIDENGRFIQGDK-TFALVADAVLKEKGGGLLVTTVATSNL 290 KA GAD G+A DGDADR +D +GR GD+ + +V D + + V T+ T+ Sbjct: 235 KANGADLGLAFDGDADRLQVVDRDGRLFNGDELLYLIVQDRLQAGQAVEGAVGTLMTNMA 294 Query: 291 LDDIAKKHGAKVMRTKVGDLIVARALYENNGTIGGEENGGVIFPEHVLGRDGAMTVAKVV 350 ++ ++ G + +R KVGD V L + T+GGE +G ++ + DG ++ +V+ Sbjct: 295 VELAFQRQGVEFVRAKVGDRYVLEELNKRKWTLGGEGSGHLLCLDRHTTGDGIVSALQVL 354 Query: 351 EIFAKSGKKFSELIDELPKYYQ----IKTKRHVEGDRHAIVNKVAEMARERGYTVDTTDG 406 +SGK S+L++ + + Q ++ ++ + HA ++ + + Sbjct: 355 AALRRSGKTLSQLLEGVSLFPQTLINVRVEKGFDWQSHAGLSAARAVIEPQ--------- 405 Query: 407 AKIIFEDGWVLVRASGTEPIIRIFSEAKSKEKAQE 441 + G VL+RASGTEP++R+ EA+ E A++ Sbjct: 406 ---LAGRGRVLIRASGTEPVVRVMVEAEKVETAEQ 437 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: 489 Number of extensions: 26 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: 448 Length adjustment: 33 Effective length of query: 422 Effective length of database: 415 Effective search space: 175130 Effective search space used: 175130 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