Align phosphopentomutase (EC 5.4.2.7) (characterized)
to candidate AZOBR_RS33725 AZOBR_RS33725 phosphomannomutase
Query= BRENDA::Q6I7B6 (450 letters) >FitnessBrowser__azobra:AZOBR_RS33725 Length = 468 Score = 167 bits (423), Expect = 7e-46 Identities = 140/459 (30%), Positives = 211/459 (45%), Gaps = 38/459 (8%) Query: 9 IRGTLWEKVTPELAMKVGMAVGTY---KSGK-ALVGRDGRTSSVMLKNAMISGLLSTGME 64 IRG + +T A VG A GT K G A +G DGR SS L+ A++ GL+STG+ Sbjct: 17 IRGIVGTTLTTADARAVGRAFGTMIVRKGGTTACIGYDGRHSSPELEEALVDGLVSTGLR 76 Query: 65 VLDADLIPTPALAWGTR-KLADAGVMITASHNPPTDNGVKVFNGDGTEFYVEQERGLEEI 123 V L PTP L + TR + AD G+MIT SHNPP NG+K+ G G Y + L I Sbjct: 77 VTRIGLGPTPMLYFATRDREADGGIMITGSHNPPEYNGIKMMLGKGP-VYGAMIQELGAI 135 Query: 124 IFSGNFRKARWDEIKPVRNVEVIPDYINAVLDFVGHETNLKVLYDGANGAGSLVAPYLLR 183 +G++ V+V Y+ +L +LK+ +D NGA + L Sbjct: 136 AAAGDYATGAGS----AERVDVQDAYVARLLKDYDGVRDLKIAWDAGNGATGEILRRLTA 191 Query: 184 EMGAKVLSVNAHVDGHFPGRKPEPRYE-NIAYLGKLVRELGVDLAIAQDGDADRIAVFDE 242 + + + + +DG FP P+P E N+ L K V E G D+ I DGD DRI D Sbjct: 192 TLPGEHILLFDAIDGDFPNHHPDPTVEKNLVDLKKAVAEHGCDIGIGFDGDGDRIGAIDH 251 Query: 243 KGNYVDEDTVIALFAKLYVEEHGGGTVVVSIDTGSRIDAVVERAGGRVVRIPLGQPHDGI 302 G V D ++A++A ++ H G T++ + + + R GG+ + G H + Sbjct: 252 LGRVVWGDQLVAIYAADVLKSHPGATIIADVKASQTLFDEIARLGGQPLMWKTG--HSLL 309 Query: 303 KRYKA-------------IFAAEPWKLVHPKFGPWIDPFVTMGLLIKLIDENGPLSELVK 349 K A IF A+ W +G + + L+ ++ GPL+ L Sbjct: 310 KAKMAETGSPLAGEMSGHIFFADKW------YGFDDALYCAVRLIGQVSRSGGPLAALRD 363 Query: 350 EIP-TYYLKKANVLCPDEYKAEVVRRAAEEVERKLSSEIKEVLTISGFRIALNDGSWILI 408 +P + +E K +VVR EV+ +L +E +V I G R+ DG W L+ Sbjct: 364 RLPEVINTPETRFQADEERKFQVVR----EVKERLKAEGAQVNDIDGVRVQTPDG-WWLL 418 Query: 409 RPSGTEPKIRVVAEAPTEKRRDELFEMAYSTVSRIVKEA 447 R S T+ + AE+ T+ + L M + + EA Sbjct: 419 RASNTQDVLVARAESSTQDGLERLKSMVVAQLEASGLEA 457 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: 537 Number of extensions: 28 Number of successful extensions: 4 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: 468 Length adjustment: 33 Effective length of query: 417 Effective length of database: 435 Effective search space: 181395 Effective search space used: 181395 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