Align phosphopentomutase (EC 5.4.2.7) (characterized)
to candidate WP_051302736.1 A3GO_RS24860 phosphoglucosamine mutase
Query= BRENDA::Q6I7B6 (450 letters) >NCBI__GCF_000428045.1:WP_051302736.1 Length = 459 Score = 153 bits (387), Expect = 1e-41 Identities = 139/472 (29%), Positives = 224/472 (47%), Gaps = 58/472 (12%) Query: 2 RLFGTAGIRGTLWE-KVTPELAMKVGMAVGTY----KSGKALVGRDGRTSSVMLKNAMIS 56 + FGT GIRG + E K+TPE M++G A G + K L+G+D R S +L++A+ + Sbjct: 4 KYFGTDGIRGRVGEGKITPEFVMRLGWAAGRVLGNGRGSKVLIGKDTRISGYLLESALEA 63 Query: 57 GLLSTGMEVLDADLIPTPALAWGTRKL-ADAGVMITASHNPPTDNGVKVFNGDGTEFYVE 115 GL++ G+++ +PTP +A+ TR L A AG++I+ASHNP DNG+K F+ +G + E Sbjct: 64 GLVAAGVDIHLLGPMPTPGIAYLTRTLHAQAGIVISASHNPHCDNGIKFFSSEGKKLPDE 123 Query: 116 QERGLEE-------IIFSGNFRKARWDEIKPVRNVEVIPDYINAVLDFVGHETNLKVLYD 168 E +E + S KA R +E I + F G +K++ D Sbjct: 124 VELAIERELDKPMTTVESEQLGKAYRVGDAAGRYIEFCKSTIPWTMSFKG----MKIVVD 179 Query: 169 GANGAGSLVAPYLLREMGAKVLSVNAHVDGHFPGRKPEPRYENIAYLGKLVRELGVDLAI 228 A+GA +AP++ RE+GA+V+++ A DG +I L K V + DL I Sbjct: 180 CAHGATYHIAPHVFREVGAEVVAIGAEPDG--LNINAGVGSTHIETLQKEVLKQQADLGI 237 Query: 229 AQDGDADRIAVFDEKGNYVDEDTVIALFA--KLYVEEHGGGTVVVSIDTGSRIDAVVERA 286 A DGD DR+ + D G+ +D D ++ + A +L GG V + T ++ + Sbjct: 238 ALDGDGDRLIMVDANGSVLDGDDILYIIACSRLRRGILNGGVVGTKM-TNFGLEHALNEH 296 Query: 287 GGRVVRIPLGQPHDGIKRYKAIFAAEPWKLVHPKFGPWI--------DPFVTMGLLIKLI 338 G +VR +G + ++R + E W L G I D ++ ++ I Sbjct: 297 GIELVRTDVGDRYI-LERLQ----LERWSLGGEPSGHIICLDRTTTGDGIISALQVLAEI 351 Query: 339 DENG----PLSELVKEIP--TYYLKKANVLCPDEYKAEVVRRAAEEVERKLSSEIKEVLT 392 +++G L + ++ P T +K NV + AE V++A E Sbjct: 352 NKSGRKLHELRDGYQKFPQVTRNVKLGNVPATELMAAESVQQAVAAAED----------- 400 Query: 393 ISGFRIALNDGSWILIRPSGTEPKIRVVAEAPTEKRRDELFEMAYSTVSRIV 444 AL +L+RPSGTEP IRV E P + + L + + +V Sbjct: 401 ------ALAGSGRVLLRPSGTEPLIRVTVEGPDDGQVQNLSQQIVDALDLLV 446 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: 490 Number of extensions: 32 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: 459 Length adjustment: 33 Effective length of query: 417 Effective length of database: 426 Effective search space: 177642 Effective search space used: 177642 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 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