Align phosphoglucomutase (alpha-D-glucose-1,6-bisphosphate-dependent) (EC 5.4.2.2); phosphomannomutase (EC 5.4.2.8) (characterized)
to candidate AZOBR_RS33725 AZOBR_RS33725 phosphomannomutase
Query= BRENDA::M1T754 (460 letters) >FitnessBrowser__azobra:AZOBR_RS33725 Length = 468 Score = 592 bits (1525), Expect = e-173 Identities = 289/449 (64%), Positives = 336/449 (74%), Gaps = 1/449 (0%) Query: 3 HKFDPTTLREYDIRGIVGKTLNPADATAIGRGFGTLLRRAGGTRAAVGYDGRHSSPLLEA 62 H F PT LREYDIRGIVG TL ADA A+GR FGT++ R GGT A +GYDGRHSSP LE Sbjct: 5 HTFHPTLLREYDIRGIVGTTLTTADARAVGRAFGTMIVRKGGTTACIGYDGRHSSPELEE 64 Query: 63 ALVQGLIASGIDVVRVGLGPTPMLYYAEAVLEVDGGIMITGSHNPPDYNGFKMVFQHRPF 122 ALV GL+++G+ V R+GLGPTPMLY+A E DGGIMITGSHNPP+YNG KM+ P Sbjct: 65 ALVDGLVSTGLRVTRIGLGPTPMLYFATRDREADGGIMITGSHNPPEYNGIKMMLGKGPV 124 Query: 123 FGEDILKIGTMAAEGDWEEGEGTVTNADIMDMYVDRLIAGYQGGA-FKVAWDAGNGAAGP 181 +G I ++G +AA GD+ G G+ D+ D YV RL+ Y G K+AWDAGNGA G Sbjct: 125 YGAMIQELGAIAAAGDYATGAGSAERVDVQDAYVARLLKDYDGVRDLKIAWDAGNGATGE 184 Query: 182 VIEKLVKFLPGEHHLLYTDVDGDFPNHHPDPTEEKNLVDLKALVAEKGLDFGIGFDGDGD 241 ++ +L LPGEH LL+ +DGDFPNHHPDPT EKNLVDLK VAE G D GIGFDGDGD Sbjct: 185 ILRRLTATLPGEHILLFDAIDGDFPNHHPDPTVEKNLVDLKKAVAEHGCDIGIGFDGDGD 244 Query: 242 RIGAIDGKGRVVWGDQLLGILAEPVLKAVPGGTIIADVKTSQALYDRVAELGGKPLMWKT 301 RIGAID GRVVWGDQL+ I A VLK+ PG TIIADVK SQ L+D +A LGG+PLMWKT Sbjct: 245 RIGAIDHLGRVVWGDQLVAIYAADVLKSHPGATIIADVKASQTLFDEIARLGGQPLMWKT 304 Query: 302 GHSLIKAKMKEVDSPLGGEMSGHIFFAWDYYGFDDAIYAAVRLMGAVRHSGKSLTELKDA 361 GHSL+KAKM E SPL GEMSGHIFFA +YGFDDA+Y AVRL+G V SG L L+D Sbjct: 305 GHSLLKAKMAETGSPLAGEMSGHIFFADKWYGFDDALYCAVRLIGQVSRSGGPLAALRDR 364 Query: 362 MPAMVNTPEMRFQVDESRKFAVIEEVLQRLEADGADINRTDGARVNTPDGWWLLRASNTQ 421 +P ++NTPE RFQ DE RKF V+ EV +RL+A+GA +N DG RV TPDGWWLLRASNTQ Sbjct: 365 LPEVINTPETRFQADEERKFQVVREVKERLKAEGAQVNDIDGVRVQTPDGWWLLRASNTQ 424 Query: 422 DVLVARAEAKDEAGLERLLKQIDTQLELS 450 DVLVARAE+ + GLERL + QLE S Sbjct: 425 DVLVARAESSTQDGLERLKSMVVAQLEAS 453 Lambda K H 0.318 0.139 0.417 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: 722 Number of extensions: 32 Number of successful extensions: 2 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: 460 Length of database: 468 Length adjustment: 33 Effective length of query: 427 Effective length of database: 435 Effective search space: 185745 Effective search space used: 185745 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 (21.7 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