Align phosphopentomutase (EC 5.4.2.7) (characterized)
to candidate Ac3H11_444 Phosphoglucosamine mutase (EC 5.4.2.10)
Query= BRENDA::Q6I7B6 (450 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_444 Length = 444 Score = 150 bits (378), Expect = 1e-40 Identities = 144/467 (30%), Positives = 224/467 (47%), Gaps = 54/467 (11%) Query: 4 FGTAGIRGTLWEK-VTPELAMKVGMAVG-----TYKSGKALVGRDGRTSSVMLKNAMISG 57 FGT GIRGT+ + +TP+ +++ AVG T + L+G+D R S ML++A+ SG Sbjct: 6 FGTDGIRGTVGQPPITPDFVLRLAHAVGRVLRQTEERPTVLIGKDTRISGYMLESALESG 65 Query: 58 LLSTGMEVLDADLIPTPALAWGTR-KLADAGVMITASHNPPTDNGVKVFNGDGTEFYVEQ 116 S G++V+ +PTP +A+ TR + A GV+I+ASHNP DNG+K F+ GT+ Sbjct: 66 FNSAGVDVVLLGPLPTPGVAYLTRAQRASLGVVISASHNPYPDNGIKFFSAQGTKLSDAW 125 Query: 117 ERGLEEIIF-------SGNFRKARWDEIKPVRNVEVIPDYINAVLDFVGHETNLKVLYDG 169 E +EE + S + KAR + R +E L G LK++ D Sbjct: 126 ELAVEEALAQSPVWADSASLGKARRLDDAAGRYIEFCKSTFPQDLTLKG----LKIVVDA 181 Query: 170 ANGAGSLVAPYLLREMGAKVLSVNAHVDGHFPGRKPEPRYENIAYLGKLVRELGVDLAIA 229 A+GA VAP + E+GA+VLS+ DG + + + L + VR D IA Sbjct: 182 AHGAAYQVAPKVFHELGAEVLSIGCAPDGLNINHEVGATHPDA--LVRAVRANRADYGIA 239 Query: 230 QDGDADRIAVFDEKGNYVDEDTVIALFA--KLYVEEHGGGTVVVSIDTGSRIDAVVERAG 287 DGDADR+ V D G + D ++ L A ++ +EH G VV ++ T ++ ++ G Sbjct: 240 LDGDADRLQVVDATGRLYNGDELLYLMASDRMGRDEHVPG-VVGTLMTNMAVEVALQSRG 298 Query: 288 GRVVRIPLGQPH--DGIKRYKAIFAAE-PWKLVHPKFGPWIDPFVT-MGLLIKLIDENGP 343 + VR +G + + + R++ + E L+ D V+ + +L + Sbjct: 299 VKFVRAKVGDRYVLEELARHRWLLGGEGSGHLLALDRHTTGDGLVSALQVLQACVRSGQT 358 Query: 344 LSELVKEIPTYYLKKANV-LCP--DEYKAEVVRRAAEEVERKLSSEIKEVLTISGFRIAL 400 L++L+ E+ Y NV L P D ++ + VER L + + Sbjct: 359 LAQLLAEVTLYPQVLLNVRLAPGQDWKSNRLLADTTQAVERDLGASGR------------ 406 Query: 401 NDGSWILIRPSGTEPKIRVVAEAPTEKRRDELFEMAYSTVSRIVKEA 447 +LIR SGTEP +RV+ EA RD EMA S R+ A Sbjct: 407 -----VLIRASGTEPLLRVMVEA-----RDA--EMASSCAQRLADAA 441 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: 446 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: 450 Length of database: 444 Length adjustment: 33 Effective length of query: 417 Effective length of database: 411 Effective search space: 171387 Effective search space used: 171387 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