Align phosphopentomutase (EC 5.4.2.7) (characterized)
to candidate WP_057687434.1 ABB28_RS16370 phosphomannomutase/phosphoglucomutase
Query= BRENDA::Q6I7B6 (450 letters) >NCBI__GCF_001431535.1:WP_057687434.1 Length = 779 Score = 149 bits (375), Expect = 4e-40 Identities = 139/462 (30%), Positives = 203/462 (43%), Gaps = 55/462 (11%) Query: 3 LFGTAGIRGTLWEKVTPELAMKVGMAVGTYKSGKAL----VGRDGRTSSVMLKNAMISGL 58 +F IRG + E++TP++A +G A+G+ + L +GRDGR S L + GL Sbjct: 322 IFRAYDIRGVVGEELTPKVAALIGQAIGSEVLAQGLREVVIGRDGRLSGPELAAGLAEGL 381 Query: 59 LSTGMEVLDADLIPTPALAWGTRKLADAG-VMITASHNPPTDNGVKV------FNGDGTE 111 G +V+D L PTP + + + L V +T SHNPP NG K+ +GD Sbjct: 382 RRAGCDVIDIGLAPTPVVYFASHHLRTGSCVAVTGSHNPPEYNGFKIVIAGQTLSGDAVT 441 Query: 112 FYVEQ--ERGLEEIIFSGNFRKARWDEIKPVRNVEVIPDYINAVLDFVGHETNLKVLYDG 169 ++ E L + GN+++ EV DY+ + D V E LKV+ D Sbjct: 442 ALYQRIVEGRLAQASSPGNYQQR-----------EVNDDYVRRIADDVQLERPLKVVADA 490 Query: 170 ANG-AGSLVAPYLLREMGAKVLSVNAHVDGHFPGRKPEP-RYENIAYLGKLVRELGVDLA 227 NG AG+LV P LL +GA V+ + VDG+FP P+P N+ L + V+ DL Sbjct: 491 GNGVAGALVQP-LLEAIGADVIPLYCDVDGNFPNHHPDPSEPANLQDLVQTVKRFDADLG 549 Query: 228 IAQDGDADRIAVFDEKGNYVDEDTVIALFAKLYVEEHGGGTVVVSIDTGSRIDAVVERAG 287 IA DGD DR+ V G + D ++ LFA + + G V+ + ++ V R G Sbjct: 550 IAFDGDGDRLGVVTPDGTIIFADRLLMLFAADVLLRNPGAMVIYDVKCTGKLADFVLRHG 609 Query: 288 GRVVRIPLGQPHDGIKRYKA-------------IFAAEPWKLVHPKFGPWIDPFVTMGLL 334 G + G H IK A F E W FG + LL Sbjct: 610 GSPMMWKTG--HSLIKARMAETDAELAGEMSGHFFFRERW------FGFDDGLYAAARLL 661 Query: 335 -IKLIDENGP---LSELVKEIPTYYLKKANVLCPDEYKAEVVRRAAEEVERKLSSEIKEV 390 I + E P L EL + I T +K +V AA+ + + Sbjct: 662 EILALREETPQEVLEELPQSISTPEIKVPVADGTPHALVSLVVSAAQSGDNPFVG--GRI 719 Query: 391 LTISGFRIALNDGSWILIRPSGTEPKIRVVAEAPTEKRRDEL 432 TI G R+ DG W L+R S T P + + EA TE+ + + Sbjct: 720 STIDGLRVDFADG-WGLVRASNTTPVLVLRFEADTEEALERI 760 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: 821 Number of extensions: 50 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 450 Length of database: 779 Length adjustment: 37 Effective length of query: 413 Effective length of database: 742 Effective search space: 306446 Effective search space used: 306446 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