Align phosphomannose mutase (EC 5.4.2.8) (characterized)
to candidate WP_011988885.1 CKL_RS01555 phosphoglucosamine mutase
Query= metacyc::MONOMER-13382 (455 letters) >NCBI__GCF_000016505.1:WP_011988885.1 Length = 449 Score = 255 bits (652), Expect = 2e-72 Identities = 177/476 (37%), Positives = 257/476 (53%), Gaps = 48/476 (10%) Query: 1 MGKLFGTFGVRGIANEKITPEFAMKIGMAFGTLLKREGR-KKPLVVVGRDTRVSGEMLKE 59 M ++FGT GVRGIAN+++TPE A K+G A +L GR KP ++VG DTR+SG+ML+ Sbjct: 1 MHRMFGTDGVRGIANKELTPELAYKLGKAGAYVLT--GRCHKPKILVGMDTRISGDMLEN 58 Query: 60 ALISGLLSVGCDVIDVGIAPTPAVQWATKHFNADGGAVITASHNPPEYNGIKLLEPNGMG 119 AL+SG+LS+G + I VGI PTPAV + T+ +NAD G VI+ASHNP EYNGIK G Sbjct: 59 ALVSGILSIGAEAICVGIVPTPAVAYLTRKYNADAGVVISASHNPVEYNGIKFFNGKGYK 118 Query: 120 LKKEREAIVEELFFKEDFDRA---------KWYEIGEVRREDIIKPYIEAIKSKVDVEAI 170 L E E ++ + D + K E GE R K YIE KS +D + + Sbjct: 119 LSDELEDKIQYVIESNFKDVSIPIGSKVGRKIMETGEAR-----KAYIEFAKSTIDTD-L 172 Query: 171 KKRKPFVVVDTSNGAGSLTLPYLLRELGCKVITVNAQPDGYFPARN-PEPNEENLKEFME 229 K K VV+D +NGA +T +ELG KV +N +PDG N + ENL M+ Sbjct: 173 KDLK--VVLDCANGASYVTSVKAFQELGAKVKVINNEPDGININHNCGSTHPENL---MK 227 Query: 230 IVKALGADFGVAQDGDADRAVFIDENGRFIQGDKTFALVADAVLKEKG---GGLLVTTVA 286 V G D G+A DGDADR + IDE G I GD A++A LK +G ++V+TV Sbjct: 228 TVVEEGYDMGLAFDGDADRCLAIDEKGNLINGDFIMAIIAKH-LKNQGKLYKNVVVSTVM 286 Query: 287 TSNLLDDIAKKHGAKVMRTKVGDLIVARALYENNGTIGGEENGGVIFPEHVLGRDGAMTV 346 ++ D K+ G ++T+VGD V + + +GGE++G +I ++ DG +T Sbjct: 287 SNVGFDIALKEEGINTIKTQVGDRYVLEEMRKEGYKLGGEQSGHIIMLDYNTTGDGLITA 346 Query: 347 AKVVEIFAKSGKKFSELIDELPKYYQIKTKRHVEGDR-------HAIVNKVAEMARERGY 399 ++ I KSG+K S++ + Q V D+ IV K+ E+ R+ Sbjct: 347 LQIACIVKKSGRKLSDIASMMKNLPQTLVNAKVPDDKKKIYMEDEEIVLKIKEIERK--- 403 Query: 400 TVDTTDGAKIIFEDGWVLVRASGTEPIIRIFSEAKSKEKAQEYLNLGIELLEKALS 455 + G VL+R SGTEP++R+ E + + + + + EL+E L+ Sbjct: 404 ----------LHGCGRVLIRPSGTEPLVRVMLEGEEQGEIDKMAHNLAELIEVKLN 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: 531 Number of extensions: 34 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: 449 Length adjustment: 33 Effective length of query: 422 Effective length of database: 416 Effective search space: 175552 Effective search space used: 175552 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 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