Align phosphopentomutase (EC 5.4.2.7) (characterized)
to candidate RR42_RS13475 RR42_RS13475 phosphoglucosamine mutase
Query= BRENDA::Q6I7B6 (450 letters) >FitnessBrowser__Cup4G11:RR42_RS13475 Length = 448 Score = 133 bits (334), Expect = 1e-35 Identities = 129/454 (28%), Positives = 211/454 (46%), Gaps = 60/454 (13%) Query: 2 RLFGTAGIRGTLWEK-VTPELAMKVGMAVGTYKSGKA----------LVGRDGRTSSVML 50 + FGT GIRG + E +TP+ M++G A G + A L+G+D R S ML Sbjct: 4 KYFGTDGIRGRVGEAPITPDFVMRLGYAAGMVLAHGAKQHDQARPTVLIGKDTRISGYML 63 Query: 51 KNAMISGLLSTGMEVLDADLIPTPALAWGTRKL-ADAGVMITASHNPPTDNGVKVFNGDG 109 + A+ +G S G+ VL +PTP +A+ TR L AGV+I+ASHNP DNG+K F+ DG Sbjct: 64 EAALEAGFTSAGVNVLLTGPLPTPGVAYLTRALRLSAGVVISASHNPYYDNGIKFFSADG 123 Query: 110 TEFYVEQERGLEEIIFSGNFRKARWDEIKPVRNVEVIP----DYINAVLDFVGHETNLKV 165 + E +E+ + R D++ R +E ++ + + LK+ Sbjct: 124 DKLPDAVEMAIEQAL-EEPMVCVRSDDLGRARRIEDAAGRYIEFCKSTFPYEQDLHKLKL 182 Query: 166 LYDGANGAGSLVAPYLLREMGAKVLSVNAHVDGHFPGRKPEPRYENIAY-------LGKL 218 + D A+GA +AP++ E+GA V+S+ G +P+ R N Y L + Sbjct: 183 VVDCAHGAAYHIAPHVFHELGADVISI---------GNQPDGRNINAGYGATAPEKLIEA 233 Query: 219 VRELGVDLAIAQDGDADRIAVFDEKGNYVDEDTVIALFA--KLYVEEHGGGTVVVSIDTG 276 V+ G DL +A DGDADR+ V D G + D ++ L +L + G V ++ T Sbjct: 234 VKANGADLGLAFDGDADRLQVVDRDGRLFNGDELLYLIVQDRLQAGQAVEG-AVGTLMTN 292 Query: 277 SRIDAVVERAGGRVVRIPLGQPH--DGIKRYKAIFAAE-PWKLVHPKFGPWIDPFVTMGL 333 ++ +R G VR +G + + + + K E L+ D V+ Sbjct: 293 MAVELAFQRQGVEFVRAKVGDRYVLEELNKRKWTLGGEGSGHLLCLDRHTTGDGIVSALQ 352 Query: 334 LIKLIDENG-PLSELVKEIPTYYLKKANVLCPD--EYKAEVVRRAAEEV-ERKLSSEIKE 389 ++ + +G LS+L++ + + NV ++++ AA V E +L+ + Sbjct: 353 VLAALRRSGKTLSQLLEGVSLFPQTLINVRVEKGFDWQSHAGLSAARAVIEPQLAGRGR- 411 Query: 390 VLTISGFRIALNDGSWILIRPSGTEPKIRVVAEA 423 +LIR SGTEP +RV+ EA Sbjct: 412 ----------------VLIRASGTEPVVRVMVEA 429 Lambda K H 0.318 0.138 0.402 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: 453 Number of extensions: 27 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 450 Length of database: 448 Length adjustment: 33 Effective length of query: 417 Effective length of database: 415 Effective search space: 173055 Effective search space used: 173055 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