Align phosphomannomutase (EC 5.4.2.8) (characterized)
to candidate WP_024851899.1 N745_RS0109535 phosphomannomutase/phosphoglucomutase
Query= BRENDA::P26276 (463 letters) >NCBI__GCF_000526715.1:WP_024851899.1 Length = 474 Score = 434 bits (1116), Expect = e-126 Identities = 226/467 (48%), Positives = 305/467 (65%), Gaps = 16/467 (3%) Query: 13 IFRAYDIRGVVGDTLTAETAYWIGRAIGSESLARGEPCVAVGRDGRLSGPELVKQLIQGL 72 IF+AYDIRG V +L A IG A + +A GE C+ VGRDGRLS L + ++G+ Sbjct: 8 IFKAYDIRGKVDISLDESAAESIGIAFAEQLIAYGETCLVVGRDGRLSSLRLQQAFMRGV 67 Query: 73 VDCGCQVSDVGMVPTPVLYYAANVLEG-KSGVMLTGSHNPPDYNGFKIVVAGETLANEQI 131 + DVG V +P++Y+AA LEG S ++TGSHNPP+ NG K+V G+ L +QI Sbjct: 68 ASQKVSIIDVGEVTSPMVYFAAETLEGVNSCAVITGSHNPPEDNGIKLVTQGQALYGQQI 127 Query: 132 QALRERIE-----------KNDLASGVGSVEQVDILPRYFKQIRDDIAMAKPMKVVVDCG 180 QALR+RI KN G S + + I Y ++I +I + +P+KVVVD G Sbjct: 128 QALRKRIGSEGFDQTLKQVKNLPGWGNSSAQNLSIFSDYRQRIASEIQLYRPLKVVVDAG 187 Query: 181 NGVAGVIAPQLIEALGCSVIPLYCEVDGNFPNHHPDPGKPENLKDLIAKVKAENADLGLA 240 NGVAG AP+++ ++GC VI L+CEVDG+FPNHHPDP K ENL DL V ADLGLA Sbjct: 188 NGVAGRYAPEVLRSIGCEVIELFCEVDGHFPNHHPDPAKLENLTDLKTAVFEHQADLGLA 247 Query: 241 FDGDGDRVGVVTNTGTIIYPDRLLMLFAKDVVSRNPGADIIFDVKCTRRLIALISGYGGR 300 FDGDGDR GV+ N G ++ PDR L+LFA+D++ G +IIFDVKC+ + + G+ Sbjct: 248 FDGDGDRCGVIDNQGLVLEPDRQLILFARDILKNRAGGEIIFDVKCSALVAQEVEKSNGK 307 Query: 301 PVMWKTGHSLIKKKMKETGALLAGEMSGHVFFKERWFGFDDGIYSAARLLEILSQDQRDS 360 VMWKTGHSL+K KMK T ALL GEMSGH+FF++RW+GFDD IY+AARL+E+L++ + + Sbjct: 308 AVMWKTGHSLMKAKMKVTSALLGGEMSGHLFFQDRWYGFDDAIYTAARLVELLARQSQTA 367 Query: 361 EHVFSAFPSDISTPEINITVTEDSKFAIIEAL----QRDAQWGEGNITTLDGVRVDYPKG 416 +F+ P STPE++I V E ++E L +++ I TLDGVRV+Y G Sbjct: 368 AELFAKIPQWQSTPELHIDVPEGEANLLVENLCQSFMKESDSEIKEIITLDGVRVEYKDG 427 Query: 417 WGLVRASNTTPVLVLRFEADTEEELERIKTVFRNQLKAVDSSLPVPF 463 WGLVRASNTT L +RFEA T++ LE+I+ F+ +L + L +PF Sbjct: 428 WGLVRASNTTSTLTIRFEATTQQGLEKIQKRFKQRLLVLAPELKLPF 474 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: 544 Number of extensions: 14 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: 463 Length of database: 474 Length adjustment: 33 Effective length of query: 430 Effective length of database: 441 Effective search space: 189630 Effective search space used: 189630 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 Apr 09 2024. 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