Align phosphomannomutase (EC 5.4.2.8) (characterized)
to candidate WP_011766504.1 AZO_RS13965 phosphomannomutase/phosphoglucomutase
Query= BRENDA::P26276 (463 letters) >NCBI__GCF_000061505.1:WP_011766504.1 Length = 463 Score = 519 bits (1336), Expect = e-152 Identities = 257/463 (55%), Positives = 329/463 (71%), Gaps = 3/463 (0%) Query: 3 TAKAPTLPA-SIFRAYDIRGVVGDTLTAETAYWIGRAIGSESLARGEPCVAVGRDGRLSG 61 T P +PA IF+AYDIRG+V TLT E IG+A+GSE+ ARG+ +AVGRDGRLSG Sbjct: 2 TQSKPFVPAPEIFKAYDIRGIVDKTLTVEAVRAIGQALGSEARARGQKAIAVGRDGRLSG 61 Query: 62 PELVKQLIQGLVDCGCQVSDVGMVPTPVLYYAANVLEGKSGVMLTGSHNPPDYNGFKIVV 121 P L L G+ G V D+G VPTP+ Y+AA L S V +TGSHNPPDYNG K+V+ Sbjct: 62 PALAGALADGIRAAGVDVVDIGCVPTPLTYFAAYHLGTDSCVSVTGSHNPPDYNGLKMVL 121 Query: 122 AGETLANEQIQALRERIEKNDLASGVGSVEQVDILPRYFKQIRDDIAMAKPMKVVVDCGN 181 G+TL EQI LR R+ + DL G G + D+ Y +++ D+ +++PMK+V+DCGN Sbjct: 122 GGQTLYGEQILDLRRRLIEGDLTEGAGELRTADVNAAYLERVTSDVKLSRPMKIVMDCGN 181 Query: 182 GVAGVIAPQLIEALGCSVIPLYCEVDGNFPNHHPDPGKPENLKDLIAKVKAENADLGLAF 241 GVAG IAP L + LGC ++ L+CEVDGNFPNHHPDP KPENL+D++ +K +A+LGLAF Sbjct: 182 GVAGAIAPALFKQLGCELVELFCEVDGNFPNHHPDPSKPENLEDVVRALKETDAELGLAF 241 Query: 242 DGDGDRVGVVTNTGTIIYPDRLLMLFAKDVVSRNPGADIIFDVKCTRRLIALISGYGGRP 301 DGDGDR+GVVT G II+PDR LMLFA+DV+SR PG +II+DVKCTR L I GG+ Sbjct: 242 DGDGDRLGVVTKDGEIIFPDRQLMLFAEDVLSRVPGGEIIYDVKCTRNLAGWIKQRGGKA 301 Query: 302 VMWKTGHSLIKKKMKETGALLAGEMSGHVFFKERWFGFDDGIYSAARLLEILSQDQRDSE 361 MW TGH+L+K K+KETGA LAGEMSGH+FFKERW+GFDDG+Y+ ARLLEILS+ D+ Sbjct: 302 TMWNTGHALVKAKLKETGAPLAGEMSGHMFFKERWYGFDDGLYAGARLLEILSR-SGDAN 360 Query: 362 HVFSAFPSDISTPEINITVTEDSKFAIIEALQRDAQW-GEGNITTLDGVRVDYPKGWGLV 420 V P +STPE+NI + E F +++ L+ AQ+ G TLDGVRV+Y G+GL Sbjct: 361 AVLKGLPDAVSTPELNIKMNEGEPFELVKRLKEQAQFDGAVERITLDGVRVEYADGFGLA 420 Query: 421 RASNTTPVLVLRFEADTEEELERIKTVFRNQLKAVDSSLPVPF 463 R SNTTPV+VLRFEA+ L RI+ FR + +V + +PF Sbjct: 421 RPSNTTPVVVLRFEANDAAALTRIQDAFRTAITSVWPGVKLPF 463 Lambda K H 0.319 0.138 0.410 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: 635 Number of extensions: 27 Number of successful extensions: 3 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: 463 Length of database: 463 Length adjustment: 33 Effective length of query: 430 Effective length of database: 430 Effective search space: 184900 Effective search space used: 184900 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 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 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