Align Phosphoglucomutase/phosphomannomutase; PGM/PMM; EC 5.4.2.2; EC 5.4.2.8 (characterized)
to candidate Pf1N1B4_1165 Phosphoglucosamine mutase (EC 5.4.2.10)
Query= SwissProt::Q68BJ6 (456 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1165 Length = 445 Score = 200 bits (509), Expect = 7e-56 Identities = 153/459 (33%), Positives = 229/459 (49%), Gaps = 29/459 (6%) Query: 3 KLFGTFGVRG-IANEEITPEFALKIGMAFGTLLKREGRERPLVVVGRDTRVSGEMLKDAL 61 K FGT G+RG + ITP+F LK+G A G + G + V+VG+DTR+SG M + AL Sbjct: 4 KYFGTDGIRGRVGQYPITPDFMLKLGWAAGMAFRSMGACK--VLVGKDTRISGYMFESAL 61 Query: 62 ISGLLSTGCDVIDVGIAPTPAIQWATNHFNADGGAVITASHNPPEYNGIKLLEPNGMGLK 121 +GL S G DV+ +G PTPAI + T F+A+ G VI+ASHNP + NGIK G L Sbjct: 62 EAGLTSAGADVMLLGPMPTPAIAYLTRTFHAEAGIVISASHNPHDDNGIKFFSGKGTKLP 121 Query: 122 KEREAIVEELFFSEDFHRAKWNEIGEL-RKEDIIKPYIEAIKNRVDVEAIKKRRPFVVVD 180 E E ++EEL + ++IG++ R D YIE K+ V +V+D Sbjct: 122 DEVELMIEEL-LDTPMTVVESSKIGKVSRINDASGRYIEFCKSSVPT-GTSFTGLKIVID 179 Query: 181 TSNGAGSLTLPYLLRELGCKVVSVNAHPDGHFPARNPEPNEENLKGFMEIVKALGADFGV 240 ++GA P + RELG +VV ++AHPDG N +++ V A AD G+ Sbjct: 180 CAHGATYKVAPSVFRELGAEVVVLSAHPDG--LNINENCGSTHMEPLQAAVLAEHADLGI 237 Query: 241 AQDGDADRAVFIDENGRFIQGDKTFALVADAVLRENG---GGLLVTTIATSNL---LDDI 294 A DGD DR +D G + GD+ ++A L+E G GG++ T ++ L L D+ Sbjct: 238 AFDGDGDRVQMVDHTGAVVDGDELLFIIA-RDLQERGKLQGGVVGTLMSNLGLELALADL 296 Query: 295 AKRNGAKVMRTKVGDLIVARALLENNGTIGGEENGGVIFPDFVLGRDGAMTTAKIVEIFA 354 A +R VGD V LLE + +GGE +G ++ D + +++ Sbjct: 297 A----IPFVRANVGDRYVISELLERDWQVGGENSGHIVCFSHTTTGDAIIAALQVLMALK 352 Query: 355 KSGKKFSELIDELPKYYQFKTKRHVEGDRKAIV-AKVAELAEKKGYKIDTTDGTKIIFDD 413 + + ++ L K Q G + KV E +++ T+ + Sbjct: 353 RRTEGLAQSRQALRKCPQVLINVRFGGGASPLEHPKVKEASDRV---------TQAMAGR 403 Query: 414 GWVLVRASGTEPIIRIFSEAKSEEKAREYLELGIKLLEE 452 G VL+R SGTEP++R+ E + E + R Y E KL+ E Sbjct: 404 GRVLLRKSGTEPLVRVMVEGEDETQVRGYAEELAKLVTE 442 Lambda K H 0.317 0.139 0.396 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: 504 Number of extensions: 34 Number of successful extensions: 5 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: 456 Length of database: 445 Length adjustment: 33 Effective length of query: 423 Effective length of database: 412 Effective search space: 174276 Effective search space used: 174276 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