Align phosphopentomutase (EC 5.4.2.7) (characterized)
to candidate GFF4692 PS417_24005 phosphoglucosamine mutase
Query= BRENDA::Q6I7B6 (450 letters) >FitnessBrowser__WCS417:GFF4692 Length = 445 Score = 138 bits (347), Expect = 4e-37 Identities = 130/445 (29%), Positives = 208/445 (46%), Gaps = 42/445 (9%) Query: 2 RLFGTAGIRGTLWE-KVTPELAMKVGMAVG----TYKSGKALVGRDGRTSSVMLKNAMIS 56 + FGT GIRG + E +TP+ +K+G A G + + + LVG+D R S M ++A+ + Sbjct: 4 KYFGTDGIRGRVGEFPITPDFMLKLGWAAGMAFRSMGACRILVGKDTRISGYMFESALEA 63 Query: 57 GLLSTGMEVLDADLIPTPALAWGTRKL-ADAGVMITASHNPPTDNGVKVFNGDGTEFYVE 115 GL + G +VL +PTPA+A+ TR A+AG++I+ASHNP DNG+K F+G GT+ E Sbjct: 64 GLSAAGADVLLLGPMPTPAIAYLTRTFHAEAGIVISASHNPHDDNGIKFFSGQGTKLPDE 123 Query: 116 QERGLEE-------IIFSGNFRKARWDEIKPVRNVEVIPDYINAVLDFVGHETNLKVLYD 168 E +EE ++ S K R +E + + F G LK++ D Sbjct: 124 IELMIEELLDAPMTVVESSKLGKVSRINDASGRYIEFCKSSVPSSTSFAG----LKLVVD 179 Query: 169 GANGAGSLVAPYLLREMGAKVLSVNAHVDGHFPGRKPEPRYENIAYLGKLVRELGVDLAI 228 A+GA VAP + +E+GA+V ++A DG ++ L V DL I Sbjct: 180 CAHGATYKVAPSVFKELGAQVTVLSAQPDG--LNINENCGSTHMEQLQAAVLAEHADLGI 237 Query: 229 AQDGDADRIAVFDEKGNYVDEDTVIALFAK-LYVEEHGGGTVVVSIDTGSRIDAVVERAG 287 A DGD DR+ + D G VD D ++ + A+ L+ + G VV ++ + ++ + G Sbjct: 238 AFDGDGDRVLMVDHTGAIVDGDELLFIIARDLHERDRLQGGVVGTLMSNLGLELALSDLG 297 Query: 288 GRVVRIPLGQPH---DGIKRYKAIFAAEPWKLV---HPKFGPWIDPFVTMGLLIKLIDEN 341 VR +G + + ++R I +V H G I + +L+ L Sbjct: 298 IPFVRANVGDRYVIAELLERNWLIGGENSGHVVCFQHTTTGDAI--IAALQVLMALRARG 355 Query: 342 GPLSELVKEIPTYYLKKANVLCPDEYKAEVVRRAAEEVERKLSSEIKEVLTISGFRIALN 401 L++ ++A CP +E E E +T +A+ Sbjct: 356 ESLAQ---------SRQALRKCPQVLLNVRFSGGENPIEHPAVKEACERVT-----LAMA 401 Query: 402 DGSWILIRPSGTEPKIRVVAEAPTE 426 +L+R SGTEP +RV+ E E Sbjct: 402 GRGRVLLRKSGTEPLVRVMVEGDDE 426 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: 430 Number of extensions: 24 Number of successful extensions: 5 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: 445 Length adjustment: 33 Effective length of query: 417 Effective length of database: 412 Effective search space: 171804 Effective search space used: 171804 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