Align phosphomannose mutase (EC 5.4.2.8) (characterized)
to candidate 6936771 Sama_0956 phosphoglucosamine mutase (RefSeq)
Query= metacyc::MONOMER-13382 (455 letters) >FitnessBrowser__SB2B:6936771 Length = 445 Score = 223 bits (568), Expect = 1e-62 Identities = 159/453 (35%), Positives = 235/453 (51%), Gaps = 33/453 (7%) Query: 3 KLFGTFGVRG-IANEKITPEFAMKIGMAFGTLLKREGRKKPLVVVGRDTRVSGEMLKEAL 61 K FGT G+RG + +++TPE A+K+G A G +L R G KK V++G+DTR+SG M + AL Sbjct: 5 KFFGTDGIRGKVGADQMTPELALKLGWAAGRVLARTGTKK--VIIGKDTRISGYMFESAL 62 Query: 62 ISGLLSVGCDVIDVGIAPTPAVQWATKHFNADGGAVITASHNPPEYNGIKLLEPNGMGLK 121 +G S G +V+ +G PTPAV + T+ F A+ G VI+ASHNP NGIK +G L Sbjct: 63 EAGFSSAGLNVLLMGPMPTPAVAYLTRTFRAEAGVVISASHNPYYDNGIKFFSNDGSKLD 122 Query: 122 KEREAIVEELFFKEDFDRAKWYEIGEVRR-EDIIKPYIEAIKSKVDVEAIKKRKPFVVVD 180 E E + E ++ A+ +G+V R +D YIE K + +VVD Sbjct: 123 DEIELAI-EAELEKPLICAESQFLGKVSRIDDARGRYIEYCKGNFPADQTLSGLK-IVVD 180 Query: 181 TSNGAGSLTLPYLLRELGCKVITVNAQPDGYFPARNPEPNEENLKEFMEIVKALGADFGV 240 ++GA P + RELG +V+ + +P+G N + ++ + V + AD G+ Sbjct: 181 CAHGATYHIAPAVFRELGAEVVAIGVEPNGM--NINDKCGATSMGAIRDKVLEVNADLGI 238 Query: 241 AQDGDADRAVFIDENGRFIQGDK-TFALVADAVLKEKG---GGLLVTTVATSNLLDDIAK 296 A DGD DR + + + G I GD+ + L DA KE+G GG++ T +A L+ K Sbjct: 239 ALDGDGDRIMMVTQEGDIIDGDQILYILALDA--KERGLLKGGVVGTQMANLG-LELALK 295 Query: 297 KHGAKVMRTKVGDLIVARALYENNGTIGGEENGGVIFPEHVLGRDGAMTVAKVVEIFAKS 356 G R+KVGD V L E IGGE +G ++ +H DG + V+ +S Sbjct: 296 DEGIPFARSKVGDRYVMELLKELGWRIGGENSGHILNLDHGTTGDGIVAGILVLAAMRRS 355 Query: 357 GKKFSELIDELPKYYQIKTKRHVEGDRH-----AIVNKVAEMARERGYTVDTTDGAKIIF 411 GK +LI +L + Q+ EGD++ + KVAE+ RE G Sbjct: 356 GKGLQQLIAKLKMFPQVLVNVRFEGDKNPLEADTVTAKVAEVERELG------------- 402 Query: 412 EDGWVLVRASGTEPIIRIFSEAKSKEKAQEYLN 444 E G VL+R SGTEP++R+ E + KE N Sbjct: 403 ERGRVLLRKSGTEPLLRVMVEGEDKETVTRLAN 435 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: 509 Number of extensions: 29 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: 445 Length adjustment: 33 Effective length of query: 422 Effective length of database: 412 Effective search space: 173864 Effective search space used: 173864 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