Align phosphomannomutase (EC 5.4.2.8) (characterized)
to candidate 8501959 DvMF_2673 Phosphomannomutase (RefSeq)
Query= BRENDA::P26276 (463 letters) >FitnessBrowser__Miya:8501959 Length = 464 Score = 395 bits (1016), Expect = e-114 Identities = 206/445 (46%), Positives = 273/445 (61%), Gaps = 6/445 (1%) Query: 14 FRAYDIRGVVGDTLTAETAYWIGRAIGSESLARGEPCVAVGRDGRLSGPELVKQLIQGLV 73 FRAYDIRG+V AE +GRA G+ L RG VG D R S P L GL+ Sbjct: 9 FRAYDIRGIVDADFDAEWVERLGRACGTYLLERGIGAAVVGHDCRHSSPAYHDALTAGLI 68 Query: 74 DCGCQVSDVGMVPTPVLYYAANVLEGKSGVMLTGSHNPPDYNGFKIVVAGETLANEQIQA 133 CG V VGMVPTP+LY+A LE + G+M+T SHNPP+YNGFK+ T+ +I+ Sbjct: 69 ACGIDVVSVGMVPTPLLYFAVRHLERQGGIMITASHNPPEYNGFKVWAGQTTIHTTEIRR 128 Query: 134 LRERIEKNDLASGVGSVEQVDILPRYFKQIRDDIAMAK----PMKVVVDCGNGVAGVIAP 189 + E ASG G +DI+P Y + + + +A P+KVVVD GNG G I Sbjct: 129 IYEIFAAGRFASGKGVGCTMDIVPAYMEAVTQRVQLAPRARGPLKVVVDGGNGAGGDICA 188 Query: 190 QLIEALGCSVIPLYCEVDGNFPNHHPDPGKPENLKDLIAKVKAENADLGLAFDGDGDRVG 249 L+ LG VI YC+ DG FPNHHPDP N++DLIA+V +E ADLG+ DGD DR+G Sbjct: 189 DLLRRLGADVIEQYCDPDGAFPNHHPDPVVEANMRDLIARVASEGADLGIGLDGDADRLG 248 Query: 250 VVTNTGTIIYPDRLLMLFAKDVVSRNPGADIIFDVKCTRRLIALISGYGGRPVMWKTGHS 309 V G +++ D LL LFA+D+++R PG +++ DVKC+ RL I +GG+P MW TGHS Sbjct: 249 AVDAQGRLLFGDELLSLFARDLLARVPGGEVMADVKCSHRLFRDIEAHGGKPTMWITGHS 308 Query: 310 LIKKKMKETGALLAGEMSGHVFFKERWFGFDDGIYSAARLLEILSQDQRDSEHVFSAFPS 369 ++K +M E A LAGEMSGH+FF E W+GFDD IY+AA LL ILS +P Sbjct: 309 VMKARMLEVNAPLAGEMSGHMFFNEGWYGFDDAIYAAALLLRILSASDVPLT-ALPGWPP 367 Query: 370 DISTPEINITVTEDSKFAIIEALQRDAQWGEGNITTLDGVRVDYPKGWGLVRASNTTPVL 429 +TPE+++ ++ KFA++ Q + ++ +DG R+ +P GW LVRASNT PVL Sbjct: 368 SHATPELHMPCPDELKFAVVSRAQEHFR-ALYDVNEIDGARITWPDGWALVRASNTQPVL 426 Query: 430 VLRFEADTEEELERIKTVFRNQLKA 454 VLRFEA+T E L I+T+ L A Sbjct: 427 VLRFEAETPERLAEIRTLVETPLAA 451 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: 588 Number of extensions: 27 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: 464 Length adjustment: 33 Effective length of query: 430 Effective length of database: 431 Effective search space: 185330 Effective search space used: 185330 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 17 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