Align phosphomannose mutase (EC 5.4.2.8) (characterized)
to candidate HSERO_RS06955 HSERO_RS06955 phosphoglucosamine mutase
Query= metacyc::MONOMER-13382 (455 letters) >FitnessBrowser__HerbieS:HSERO_RS06955 Length = 444 Score = 214 bits (546), Expect = 3e-60 Identities = 154/455 (33%), Positives = 225/455 (49%), Gaps = 42/455 (9%) Query: 3 KLFGTFGVRG-IANEKITPEFAMKIGMAFGTLLKR--EGRKKPLVVVGRDTRVSGEMLKE 59 K FGT GVRG + ITP+F M++G A G +L + +G +P V++G+DTR+SG ML+ Sbjct: 4 KYFGTDGVRGRVGVAPITPDFVMRLGYAAGKVLAKAKDGMTRPTVLIGKDTRISGYMLEA 63 Query: 60 ALISGLLSVGCDVIDVGIAPTPAVQWATKHFNADGGAVITASHNPPEYNGIKLLEPNGMG 119 AL +G + G DV G PTPAV + T+ G VI+ASHNP NGIK +G Sbjct: 64 ALEAGFAAAGVDVWLAGPLPTPAVAYLTRALRLSAGVVISASHNPYHDNGIKFFSASGNK 123 Query: 120 LKKEREAIVEELFFKEDFDRAKWYEIGEVRR-EDIIKPYIEAIKSKVDVEAIKKRKPFVV 178 L EA +E ++ D ++G+ RR D YIE KS A+ R +V Sbjct: 124 LPDSVEADIEAA-LEQPMDCVPSEKLGKARRLSDAPGRYIEFCKSTFP-NAMNLRGMRLV 181 Query: 179 VDTSNGAGSLTLPYLLRELGCKVITVNAQPDGYFPARNPEPNEENLKEFMEIVKALGADF 238 VD ++GA P++ ELG +VIT+ QPDG N + K + V+ AD Sbjct: 182 VDCAHGAAYNIAPHVFHELGAEVITIGNQPDGL--NINEDCGATAPKTLVASVREYRADL 239 Query: 239 GVAQDGDADRAVFIDENGRFIQGDKTFALVADAVLKEKGGGLLVTTVATSNLLDDIAKKH 298 G+A DGDADR + +D GR GD+ L+ L V T+ T+ L+ KK Sbjct: 240 GIALDGDADRLIMVDGEGRIYNGDELLYLMVKDRLATGPVHGAVGTLMTNMALEVAFKKM 299 Query: 299 GAKVMRTKVGDLIVARALYENNGTIGGEENGGVI-FPEHVLGRDGAMTVAKVVEIFAKSG 357 G R KVGD V L E +GGE +G ++ +H G DG ++ +V+ +SG Sbjct: 300 GVPFERAKVGDRYVLEVLQEKGWVLGGEGSGHLLALDKHTTG-DGIVSALQVLSALKRSG 358 Query: 358 KKFSELIDELPKY------------YQIKTKRHVEGDRHAIVNKVAEMARERGYTVDTTD 405 K +EL ++ Y Y K+ ++ ++ A+ ++ E R Sbjct: 359 KTLAELTSDISMYPQSLVNVKIPAGYDWKSNTALQAEKAAVEEELGERGR---------- 408 Query: 406 GAKIIFEDGWVLVRASGTEPIIRIFSEAKSKEKAQ 440 VL+R SGTEP+IR+ EA+ + A+ Sbjct: 409 ----------VLLRPSGTEPLIRVMVEAQQADLAR 433 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: 454 Number of extensions: 28 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: 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