Align phosphopentomutase (EC 5.4.2.7) (characterized)
to candidate WP_051302238.1 A3GO_RS0112315 phosphomannomutase/phosphoglucomutase
Query= BRENDA::Q6I7B6 (450 letters) >NCBI__GCF_000428045.1:WP_051302238.1 Length = 839 Score = 181 bits (459), Expect = 8e-50 Identities = 134/437 (30%), Positives = 215/437 (49%), Gaps = 23/437 (5%) Query: 3 LFGTAGIRGTLWEKVTPELAMKVGMAVGT--YKSGK--ALVGRDGRTSSVMLKNAMISGL 58 +F IRG + E +T ++ ++G A+G+ Y+ G+ +V RDGR S A+ GL Sbjct: 388 IFRAYDIRGVVGETLTEQIVYELGRAIGSEAYEQGEQTVIVARDGRHSGAAFSKALSEGL 447 Query: 59 LSTGMEVLDADLIPTPALAWGTRKLAD-AGVMITASHNPPTDNGVKVFNGDGTEFYVEQE 117 +++G +VLD ++PTP L + T L GVMIT SHNPP NG+K+ +G + Sbjct: 448 MASGRDVLDIGMVPTPVLYFATHFLGSKTGVMITGSHNPPNYNGLKIVI-NGAALSGDAI 506 Query: 118 RGLEEIIFSGNFRKARWDEIKPVRNVEVIPDYINAVLDFVGHETNLKVLYDGANGAGSLV 177 GL++ I ++++ R + +++PDYI V+ V LK++ D NG S+V Sbjct: 507 SGLKQRIERQDYQQGRGS----LHEQDLLPDYIERVVGDVQLSRPLKLVVDCGNGVASVV 562 Query: 178 APYLLREMGAKVLSVNAHVDGHFPGRKPEP-RYENIAYLGKLVRELGVDLAIAQDGDADR 236 AP L + +G +V ++ VDG FP P+P + EN+A L VRE DL +A DGD DR Sbjct: 563 APALFQALGCEVTALYCKVDGDFPNHHPDPGKPENLADLIVAVRERKADLGVAFDGDGDR 622 Query: 237 IAVFDEKGNYVDEDTVIALFAKLYVEEHGGGTVVVSIDTGSRIDAVVERAGGRVVRIPLG 296 + V D G + D ++ L A+ + GG V+ + + + + GGR + G Sbjct: 623 LGVVDGNGKVIWPDRLLMLLARDVLSRQPGGDVIYDVKSSRHLADEILSYGGRPIMWKTG 682 Query: 297 QPHDGIK----RYKAIFAAE--PWKLVHPKFGPWIDPFVTMGLLIKLI-DENGPLSELVK 349 H IK A+ A E + ++ + D + L++L+ E P++E+ Sbjct: 683 --HSLIKAKMRETGALLAGEMSGHIFIQERWYGFDDGLYSCARLLELLSSEPVPVTEIFD 740 Query: 350 EIPTYYLKKANVLCPDEYKAEVVRRAAEEVERKLSSEIKEVLTISGFRIALNDGSWILIR 409 +P L D+ A E + + ++ TI G R+ DG W L+R Sbjct: 741 SLPESVSTPELNLAFDQEGANFA--LMESLAGQADFTDAKITTIDGLRVEFEDG-WGLVR 797 Query: 410 PSGTEPKIRVVAEAPTE 426 PS T P + EA +E Sbjct: 798 PSNTTPSVVFRFEADSE 814 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: 839 Number of extensions: 53 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: 839 Length adjustment: 37 Effective length of query: 413 Effective length of database: 802 Effective search space: 331226 Effective search space used: 331226 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: 53 (25.0 bits)
This GapMind analysis is from Sep 24 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