Align phosphomannose mutase (EC 5.4.2.8) (characterized)
to candidate 206723 DVU1282 phosphoglucosamine mutase
Query= metacyc::MONOMER-13382 (455 letters) >MicrobesOnline__882:206723 Length = 450 Score = 227 bits (579), Expect = 5e-64 Identities = 159/467 (34%), Positives = 242/467 (51%), Gaps = 36/467 (7%) Query: 3 KLFGTFGVRGIAN-EKITPEFAMKIGMAFGTLLKREGRKKPLVVVGRDTRVSGEMLKEAL 61 +LFGT G+RG N +T + A+++G+A GT R G ++ VV+G+DTR+SG M + AL Sbjct: 4 RLFGTDGLRGQVNIYPMTADMALRLGLAAGTRF-RNGNRRHRVVIGKDTRLSGYMFESAL 62 Query: 62 ISGLLSVGCDVIDVGIAPTPAVQWATKHFNADGGAVITASHNPPEYNGIKLLEPNGMGLK 121 +GL + G DV VG PTPA+ + T++ AD G VI+ASHNP NGIK + +G L Sbjct: 63 TAGLCAAGMDVFQVGPLPTPAISFLTRNMRADLGVVISASHNPFMDNGIKFFDRSGFKLP 122 Query: 122 KEREAIVEELFFKED--FDRAKWYEIGEVRR-EDIIKPYIEAIKSKVDVEAIKKRKPFVV 178 + E + ++ D +D ++G + D YI IKS + + VV Sbjct: 123 DDVENQMTDMVLDPDWQWDYPASEKVGRAYKIADAPGRYIVYIKSSFPAD-LTLDGLRVV 181 Query: 179 VDTSNGAGSLTLPYLLRELGCKVITVNAQPDGYFPARNPEPNEENLKEFMEIVKA----L 234 +D +NGA P L ELG +VI + +P+G N + + E+V A Sbjct: 182 IDCANGANYKVAPLALEELGAEVIKLGTEPNGL------NINHQCGSLYPEVVAAKVRET 235 Query: 235 GADFGVAQDGDADRAVFIDENGRFIQGDKTFALVA-DAVLKEK-GGGLLVTTVATSNLLD 292 AD G+A DGDADR + +DE G + GD+ AL A D + K K G +LV TV ++ L+ Sbjct: 236 RADIGLALDGDADRLIVVDEKGTILDGDQIMALCAQDLMAKGKLPGNMLVATVMSNMALE 295 Query: 293 DIAKKHGAKVMRTKVGDLIVARALYENNGTIGGEENGGVIFPEHVLGRDGAMTVAKVVEI 352 K+HG ++RT VGD V A+ ++ +GGE++G +IF E+ DG + +++ I Sbjct: 296 VFMKEHGGTLLRTAVGDRYVVEAMRQHGALLGGEQSGHLIFREYSTTGDGLLAALQILRI 355 Query: 353 FAKSGKKFSELIDELPKYYQIKTKRHVE-----GDRHAIVNKVAEMARERGYTVDTTDGA 407 + GK SEL +L + Q HVE + + + VA + E G Sbjct: 356 MRERGKPLSELAGQLQLFPQQLINVHVERKIPFAECQPVADAVAAIETELG--------- 406 Query: 408 KIIFEDGWVLVRASGTEPIIRIFSEAKSKEKAQEYLNLGIELLEKAL 454 + G VL+R SGTE + R+ E + E+ + E ++K L Sbjct: 407 ----DRGRVLLRYSGTESVCRVMVEGEHPEQVARLAEMLAETVQKHL 449 Lambda K H 0.317 0.138 0.391 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: 491 Number of extensions: 21 Number of successful extensions: 6 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: 455 Length of database: 450 Length adjustment: 33 Effective length of query: 422 Effective length of database: 417 Effective search space: 175974 Effective search space used: 175974 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 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