Align Mannose-6-phosphate isomerase; EC 5.3.1.8 (characterized, see rationale)
to candidate CCNA_03732 CCNA_03732 N-acyl-D-glucosamine 2-epimerase
Query= uniprot:P29954 (387 letters) >FitnessBrowser__Caulo:CCNA_03732 Length = 386 Score = 342 bits (877), Expect = 1e-98 Identities = 179/370 (48%), Positives = 223/370 (60%), Gaps = 5/370 (1%) Query: 12 LAGWLNDAALPLWRQKGFDGEGGGFVETIDMKGEPTRDDRRSRVQPRQVYCFAAAGRRGW 71 L W +AA P+W + G D GGF E ID+ G+ RR RV PRQ+Y +A AG GW Sbjct: 15 LKTWAVEAAYPIWWEVGADRVKGGFFEKIDLDGQAVDGPRRGRVLPRQIYAYAIAGDLGW 74 Query: 72 DGDWRTAAEGGLLYFDRVYGQPGGFYGALANADGKLIDASFDLYNQAFALLAFAHLAEVL 131 G WR A E GL YF Y + G + L +G+ +D + DLY+QAFAL A A +A+ L Sbjct: 75 RGPWRAAVEHGLAYFLSAYRRSDGQFRTLVGPNGESLDDTADLYDQAFALFALAAVAKAL 134 Query: 132 PERGAEMVGRSDKLRRQLEARCKHPLAGFEEDDPPRLPLGSNPHMHLFEACLASEEVEGF 191 P+R + + +R +L A KHP+AGF + +PP PL SNPHMHLFEA LA E++ Sbjct: 135 PDRADDARTLALVVRERLIAERKHPVAGFHQTNPPSAPLQSNPHMHLFEAMLAWNEID-- 192 Query: 192 DRVAWANLADEIAHLAMDRFIDAESGALREFFDHDWAPFPGEKGRIVEPGHLFEWAWLLL 251 W LADEIA LA+ RFI A SG +REFFD DW P PG GRI EPGH FEW WLL+ Sbjct: 193 KDPIWRTLADEIAELALSRFIHAPSGQIREFFDLDWNPAPGVAGRICEPGHQFEWGWLLM 252 Query: 252 RWAERRGNAQAIVKARRLFEIGEKDGTCPDRDVVVMTLFDDFSVADPTARLWPQTEWLKA 311 RW + G A A A R+ + E G R V + L DDFS D ARLWPQTE +KA Sbjct: 253 RWGQLAGRADATAAALRMIDDAETHGVDLSRGVAINALLDDFSTHDDGARLWPQTERIKA 312 Query: 312 AIRFAALTEGAERERYLASAGRAAAALQRFLNVPVRGLWRDKQKADGSFVEEPAPASTFY 371 A+ A +T A RY A AA L +L + GLWRDK + D +F+EEP PAS+FY Sbjct: 313 AVLAAEITGQA---RYWDMAAAAAEGLMAYLRTAIPGLWRDKYQPDETFIEEPVPASSFY 369 Query: 372 HILCAIYELE 381 HI AI E++ Sbjct: 370 HIALAILEMD 379 Lambda K H 0.323 0.139 0.448 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: 484 Number of extensions: 18 Number of successful extensions: 3 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: 387 Length of database: 386 Length adjustment: 30 Effective length of query: 357 Effective length of database: 356 Effective search space: 127092 Effective search space used: 127092 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 (21.9 bits) S2: 50 (23.9 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