Align phosphopentomutase (EC 5.4.2.7) (characterized)
to candidate 5210391 Shew_2832 phosphoglucosamine mutase (RefSeq)
Query= BRENDA::Q6I7B6 (450 letters) >FitnessBrowser__PV4:5210391 Length = 443 Score = 142 bits (357), Expect = 3e-38 Identities = 134/448 (29%), Positives = 212/448 (47%), Gaps = 56/448 (12%) Query: 2 RLFGTAGIRGTLWE-KVTPELAMKVGMAVGTYKSG----KALVGRDGRTSSVMLKNAMIS 56 + FGT GIRG + K+TPELA+K+G A G S K ++G+D R S + ++AM + Sbjct: 3 KFFGTDGIRGKVGAGKMTPELALKLGWAAGRVLSRTGTKKVIIGKDTRISGYLFESAMEA 62 Query: 57 GLLSTGMEVLDADLIPTPALAWGTRKL-ADAGVMITASHNPPTDNGVKVFNGDGT----E 111 GL + G+ V+ +PTPA+A+ TR A+AGV+I+ASHNP DNG+K F+ DG+ E Sbjct: 63 GLSAAGLNVMLMGPMPTPAVAYLTRTFRAEAGVVISASHNPYYDNGIKFFSTDGSKLDDE 122 Query: 112 FYVEQERGLE---EIIFSGNFRKARWDEIKPVRNVEVIPDYINAVLDFVGHETNLKVLYD 168 +E ER LE E + S K E R +E A G LK++ D Sbjct: 123 VELEIERELEKPLECVESHLLGKVSRIEDAAGRYIEYCKGNFPAEHTLNG----LKIVVD 178 Query: 169 GANGAGSLVAPYLLREMGAKVLSVNAHVDGHFPGRKPEPRYENIAYLGKLVRELGVDLAI 228 A+GA +AP + RE+GA+V+++ DG E ++ + + V DL I Sbjct: 179 CAHGATYHIAPSVFRELGAEVITIGDKPDG--ININHEVGATSMGKIRETVIAEKADLGI 236 Query: 229 AQDGDADRIAVFDEKGNYVDEDTVIALFAKLYVEEHG--GGTVVVSIDTGSRIDAVVERA 286 A DGD DRI + + G +D D ++ + A ++ G G VV ++ + +D ++ Sbjct: 237 ALDGDGDRIMMVNRHGKVIDGDEILYILA-CDAQDRGVLKGGVVGTLMSNLGLDLALKAR 295 Query: 287 GGRVVRIPLGQPHDGIKRYKAIFAAEPWKLVHPKFGPWID-------PFVTMGLLI--KL 337 IP + G + + + W++ G ++ + G+L+ + Sbjct: 296 D-----IPFARSKVGDRYVMELLKEKDWRIGGENSGHILNLDHGTTGDGIVAGILVLAAM 350 Query: 338 IDENGPLSEL---VKEIPTYYLKKANVLCPDEYKAEVVRRAAEEVERKLSSEIKEVLTIS 394 + L EL +K +P + + +A+ V A EVE KL + Sbjct: 351 CRKQATLEELTEGIKMLPQVLVNVRFEGTHNPLEADSVLSAQAEVEAKLGERGR------ 404 Query: 395 GFRIALNDGSWILIRPSGTEPKIRVVAE 422 +L+R SGTEP IRV+ E Sbjct: 405 -----------VLLRKSGTEPLIRVMVE 421 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: 507 Number of extensions: 21 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: 443 Length adjustment: 33 Effective length of query: 417 Effective length of database: 410 Effective search space: 170970 Effective search space used: 170970 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