Align phosphopentomutase (EC 5.4.2.7) (characterized)
to candidate WP_011778730.1 MVAN_RS07420 phosphoglucosamine mutase
Query= BRENDA::Q6I7B6 (450 letters) >NCBI__GCF_000015305.1:WP_011778730.1 Length = 445 Score = 168 bits (426), Expect = 3e-46 Identities = 145/462 (31%), Positives = 213/462 (46%), Gaps = 44/462 (9%) Query: 2 RLFGTAGIRGTLWEKVTPELAMKVGMAV-------GTYKSGKALVGRDGRTSSVMLKNAM 54 RLFGT G+RG ++T ELAM +G A G + A+VGRD R S ML+ A+ Sbjct: 3 RLFGTDGVRGVANRELTAELAMALGAAAARRLGRTGAARRRVAVVGRDPRASGEMLEAAV 62 Query: 55 ISGLLSTGMEVLDADLIPTPALAWGTRKL-ADAGVMITASHNPPTDNGVKVFNGDGTEFY 113 I+G+ S G++ L ++PTPA+A+ T AD GVMI+ASHNP DNG+K+F G + Sbjct: 63 IAGIASEGVDTLRVGVLPTPAVAYLTSAYDADFGVMISASHNPMPDNGIKIFGPGGHKLD 122 Query: 114 VEQERGLEEIIFSGNFRKARWDEIKPVRNVEVIPDYINAVLDFVGHETN-----LKVLYD 168 E +EE++ G + I V + E D + L VG L V+ D Sbjct: 123 DATEDRIEELVHQGPGSRPTGAGIGRVVDAE---DALERYLRHVGKAATTRLDALTVVVD 179 Query: 169 GANGAGSLVAPYLLREMGAKVLSVNAHVDGHFPGRKPEPRYENIAYLGKLVRELGVDLAI 228 A+GA SL AP R GA V+ ++A DG ++ L V G DL + Sbjct: 180 CAHGAASLAAPRAYRAAGANVIPIHAEPDG--LNINDNCGSTHMQALSAAVVSYGADLGL 237 Query: 229 AQDGDADRIAVFDEKGNYVDEDTVIALFAKLYVE--EHGGGTVVVSIDTGSRIDAVVERA 286 A DGDADR D G +D D ++ + A E E T+V ++ + + + A Sbjct: 238 AHDGDADRCLAVDAHGRVIDGDAIMVVLALAMQEAGELASDTLVTTVMSNMGLHLAMRSA 297 Query: 287 GGRVVRIPLGQPHDGIKRYKAIFA---AEPWKLVHPKFGPWIDPFVT-MGLLIKLIDENG 342 G V +G + + +F+ + +V P FG D VT + L+ ++ Sbjct: 298 GIEVRTTGVGDRYVLEELRAGLFSLGGEQSGHIVLPSFGTTGDGIVTGLRLMARMAQTGR 357 Query: 343 PLSELVKEIPTYYLKKANVLCPDE---YKAEVVRRAAEEVERKLSSEIKEVLTISGFRIA 399 L+ L + + T NV D+ A+ VR A +VE + Sbjct: 358 SLAGLAEPMQTLPQVLINVEVADKATVADAQPVRDAVAQVEAE----------------- 400 Query: 400 LNDGSWILIRPSGTEPKIRVVAEAPTEKRRDELFEMAYSTVS 441 L D IL+RPSGTE +RV+ EA E ++ +VS Sbjct: 401 LGDTGRILLRPSGTEQVVRVMVEAADEDTARQMAVRVAESVS 442 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: 437 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: 445 Length adjustment: 33 Effective length of query: 417 Effective length of database: 412 Effective search space: 171804 Effective search space used: 171804 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