Align phosphomannomutase (EC 5.4.2.8) (characterized)
to candidate WP_013133918.1 ARNIT_RS00520 phosphomannomutase/phosphoglucomutase
Query= BRENDA::P26276 (463 letters) >NCBI__GCF_000092245.1:WP_013133918.1 Length = 466 Score = 308 bits (790), Expect = 2e-88 Identities = 183/450 (40%), Positives = 271/450 (60%), Gaps = 26/450 (5%) Query: 12 SIFRAYDIRGVVGDTLTAETAYWIGRAIGSESLARG---EPCVAVGRDGRLSGPELVKQL 68 SIFR YDIRG+VG+ L +++ IG +G E++ R EP V +G D R+ PEL L Sbjct: 5 SIFREYDIRGIVGNELNEQSSKLIGYYLGLEAIKRTNVQEPVVVIGYDARIHSPELFNYL 64 Query: 69 IQGLVDCGCQVSDVGMVPTPVLYYAA-NVLEGK---SGVMLTGSHNPPDYNGFKIVVAGE 124 G GC+V +GMV T V Y+A+ +G+ + VM+TGSHNP YNGFKI + Sbjct: 65 TSGFNKAGCKVLGMGMVATGVNYFASFQEFDGEKPNASVMITGSHNPSPYNGFKITINNA 124 Query: 125 TLANEQIQALRERIEKNDLAS--GVGSVEQVDILPRYFKQIRDDIAMAKPMK--VVVDCG 180 + I A+ E I N + + +++D+ Y + + A K MK +++DCG Sbjct: 125 PFFGDDIYAMGEEIINNQNMNIKDNETYKEIDVKSLYKNYMITEFAHLKGMKQKLIIDCG 184 Query: 181 NGVAGVIAPQLIEALGCSVIPLYCEVDGNFPNHHPDPGKPENLKDLIAKVKAENADLGLA 240 NGVA + +++AL + LYCE DG FPNHHPDP + +NLKD+I K+K + + G A Sbjct: 185 NGVADTVLTDILDALELNYDALYCEPDGTFPNHHPDPSEEKNLKDVIEKLKGD-YEYGFA 243 Query: 241 FDGDGDRVGVVTNTGTIIYPDRLLMLFAKDVVSRNPGADIIFDVKCTRRLIALISGYGGR 300 +DGD DR+ +T + D + +LFAK + +NP II +VKCT+ + I+ G Sbjct: 244 YDGDADRIAFLTKNHN-VKGDIMALLFAKTM--KNP--VIIGEVKCTQIMYDRIN-ENGT 297 Query: 301 PVMWKTGHSLIKKKMKETGALLAGEMSGHVFFKERWFGFDDGIYSAARLLEILSQDQRDS 360 VM+KTGHS +K K+KE A +A E+SGH+FF +R++GFDD IY+ RLLE++ D Sbjct: 298 AVMYKTGHSNLKVKLKELNADMAAEVSGHIFFNDRYYGFDDAIYATFRLLELIFNGM-DI 356 Query: 361 EHVFSAFPSDISTPEINITVTEDSKFAIIEALQRD-AQWGEG-----NITTLDGVRVDYP 414 + + P ST EI + TE+ KF ++ ++++ G+ +I +DGVR+ + Sbjct: 357 DKEIDSLPKVYSTEEIKVETTEEEKFLLMHQIKKNLITVGDDFPKILDIIEVDGVRIVFE 416 Query: 415 KGWGLVRASNTTPVLVLRFEADTEEELERI 444 +GWGLVRASNTTPVLV RFE+ T+ E+ ++ Sbjct: 417 QGWGLVRASNTTPVLVTRFES-TDLEVAKL 445 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: 518 Number of extensions: 27 Number of successful extensions: 7 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: 466 Length adjustment: 33 Effective length of query: 430 Effective length of database: 433 Effective search space: 186190 Effective search space used: 186190 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