Align phosphomannomutase (EC 5.4.2.8) (characterized)
to candidate WP_051302238.1 A3GO_RS0112315 phosphomannomutase/phosphoglucomutase
Query= BRENDA::P26276 (463 letters) >NCBI__GCF_000428045.1:WP_051302238.1 Length = 839 Score = 555 bits (1429), Expect = e-162 Identities = 266/457 (58%), Positives = 340/457 (74%), Gaps = 1/457 (0%) Query: 8 TLPASIFRAYDIRGVVGDTLTAETAYWIGRAIGSESLARGEPCVAVGRDGRLSGPELVKQ 67 +LP SIFRAYDIRGVVG+TLT + Y +GRAIGSE+ +GE V V RDGR SG K Sbjct: 383 SLPDSIFRAYDIRGVVGETLTEQIVYELGRAIGSEAYEQGEQTVIVARDGRHSGAAFSKA 442 Query: 68 LIQGLVDCGCQVSDVGMVPTPVLYYAANVLEGKSGVMLTGSHNPPDYNGFKIVVAGETLA 127 L +GL+ G V D+GMVPTPVLY+A + L K+GVM+TGSHNPP+YNG KIV+ G L+ Sbjct: 443 LSEGLMASGRDVLDIGMVPTPVLYFATHFLGSKTGVMITGSHNPPNYNGLKIVINGAALS 502 Query: 128 NEQIQALRERIEKNDLASGVGSVEQVDILPRYFKQIRDDIAMAKPMKVVVDCGNGVAGVI 187 + I L++RIE+ D G GS+ + D+LP Y +++ D+ +++P+K+VVDCGNGVA V+ Sbjct: 503 GDAISGLKQRIERQDYQQGRGSLHEQDLLPDYIERVVGDVQLSRPLKLVVDCGNGVASVV 562 Query: 188 APQLIEALGCSVIPLYCEVDGNFPNHHPDPGKPENLKDLIAKVKAENADLGLAFDGDGDR 247 AP L +ALGC V LYC+VDG+FPNHHPDPGKPENL DLI V+ ADLG+AFDGDGDR Sbjct: 563 APALFQALGCEVTALYCKVDGDFPNHHPDPGKPENLADLIVAVRERKADLGVAFDGDGDR 622 Query: 248 VGVVTNTGTIIYPDRLLMLFAKDVVSRNPGADIIFDVKCTRRLIALISGYGGRPVMWKTG 307 +GVV G +I+PDRLLML A+DV+SR PG D+I+DVK +R L I YGGRP+MWKTG Sbjct: 623 LGVVDGNGKVIWPDRLLMLLARDVLSRQPGGDVIYDVKSSRHLADEILSYGGRPIMWKTG 682 Query: 308 HSLIKKKMKETGALLAGEMSGHVFFKERWFGFDDGIYSAARLLEILSQDQRDSEHVFSAF 367 HSLIK KM+ETGALLAGEMSGH+F +ERW+GFDDG+YS ARLLE+LS + +F + Sbjct: 683 HSLIKAKMRETGALLAGEMSGHIFIQERWYGFDDGLYSCARLLELLSSEPVPVTEIFDSL 742 Query: 368 PSDISTPEINITV-TEDSKFAIIEALQRDAQWGEGNITTLDGVRVDYPKGWGLVRASNTT 426 P +STPE+N+ E + FA++E+L A + + ITT+DG+RV++ GWGLVR SNTT Sbjct: 743 PESVSTPELNLAFDQEGANFALMESLAGQADFTDAKITTIDGLRVEFEDGWGLVRPSNTT 802 Query: 427 PVLVLRFEADTEEELERIKTVFRNQLKAVDSSLPVPF 463 P +V RFEAD+E L RI+ F+ L VD L +PF Sbjct: 803 PSVVFRFEADSEAALARIQQQFQQWLLRVDPGLNLPF 839 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: 994 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: 463 Length of database: 839 Length adjustment: 37 Effective length of query: 426 Effective length of database: 802 Effective search space: 341652 Effective search space used: 341652 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: 54 (25.4 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