Align phosphomannomutase (EC 5.4.2.8) (characterized)
to candidate WP_092482818.1 BM299_RS07095 phosphomannomutase/phosphoglucomutase
Query= BRENDA::P26276 (463 letters) >NCBI__GCF_900115975.1:WP_092482818.1 Length = 459 Score = 390 bits (1001), Expect = e-113 Identities = 207/446 (46%), Positives = 270/446 (60%), Gaps = 2/446 (0%) Query: 9 LPASIFRAYDIRGVVGDTLTAETAYWIGRAIGSESLARGEPCVAVGRDGRLSGPELVKQL 68 L IFR YDIRGV LT E +GRA G+ G V VG D R+S L L Sbjct: 3 LNPDIFRQYDIRGVADRDLTPEVVELLGRAFGTYVQQYGGSEVIVGHDNRVSSERLRDNL 62 Query: 69 IQGLVDCGCQVSDVGMVPTPVLYYAANVLEGKSGVMLTGSHNPPDYNGFKIVVAGETLAN 128 + GL GC+V DVG V TP++YYA VM+TGSHNPPD NGFKI T+ Sbjct: 63 VSGLTAVGCRVIDVGQVVTPMVYYARVHFNIDGAVMITGSHNPPDENGFKISRGAGTIYG 122 Query: 129 EQIQALRERIEKNDLASGVGSVEQVDILPRYFKQIRDDIAMA-KPMKVVVDCGNGVAGVI 187 E+IQ LRE +EK + A+G G+VEQ D++ Y +R+ I + + +KVVVDCGNG AG Sbjct: 123 EEIQRLRELMEKGEFAAGSGAVEQRDVVTPYRAMLREKIQLGPRKLKVVVDCGNGTAGPF 182 Query: 188 APQLIEALGCSVIPLYCEVDGNFPNHHPDPGKPENLKDLIAKVKAENADLGLAFDGDGDR 247 APQ+++ G PLYCE D FPNH PDP K NL DL V+ ADLG+A+DGD DR Sbjct: 183 APQILQDWGVDCHPLYCESDPTFPNHQPDPVKTANLADLRRVVRERGADLGVAYDGDADR 242 Query: 248 VGVVTNTGTIIYPDRLLMLFAKDVVSRNPGADIIFDVKCTRRLIALISGYGGRPVMWKTG 307 +GVV G +I+ D L+ L+ +++++R PG I +VKC++ L + GG+P +KTG Sbjct: 243 IGVVDEKGDVIWGDGLMCLYWREILARYPGTPAIIEVKCSQALEDEVKRLGGKPFFYKTG 302 Query: 308 HSLIKKKMKETGALLAGEMSGHVFFKERWFGFDDGIYSAARLLEILSQDQRDSEHVFSAF 367 HSLIK KMKE GA+ GEMSGH+FF + ++GFDD Y+ RLL ILS + + + Sbjct: 303 HSLIKAKMKEVGAVFTGEMSGHMFFADEFYGFDDAFYATGRLLRILSNTEEPLSKLLQSV 362 Query: 368 PSDISTPEINITVTEDSKFAIIEALQRDAQWGEGNITTLDGVRVDYPKGWGLVRASNTTP 427 P ST E + T+ KF I+ L + ++ +DG RV + GWGLVRASNT P Sbjct: 363 PKYYSTAETRVPCTDRDKFRIVAELVEHFR-ARYDVIDVDGARVLFGNGWGLVRASNTQP 421 Query: 428 VLVLRFEADTEEELERIKTVFRNQLK 453 VLV R EA T E LERI + + L+ Sbjct: 422 VLVARCEAKTPEGLERICAIMKEALQ 447 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: 576 Number of extensions: 26 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: 459 Length adjustment: 33 Effective length of query: 430 Effective length of database: 426 Effective search space: 183180 Effective search space used: 183180 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