Align Glucosamine-6-phosphate deaminase [isomerizing], alternative (EC 3.5.99.6) (characterized)
to candidate GFF3734 HP15_3676 glucosamine-fructose-6-phosphate aminotransferase, isomerizing
Query= reanno::Caulo:CCNA_00453 (363 letters) >FitnessBrowser__Marino:GFF3734 Length = 610 Score = 141 bits (355), Expect = 5e-38 Identities = 120/382 (31%), Positives = 178/382 (46%), Gaps = 28/382 (7%) Query: 2 EATVLTRHETPAPTGASPPSLAPASTHMFREAGEAARVAAVQLTANAPKIQALAQRLRAN 61 + + R T GA M +E E +V + + + L Q L Sbjct: 227 DGKAVEREVTRFEHGADSADKGEYRHFMLKEIYEQPKVIKATMEGRVTRTRVLEQALGTE 286 Query: 62 PP------RVVVTCARGSSDHAATFARYLIETKAGVLTSSAGPSVSSVYDASPNL--EGA 113 R V A G+S HA ARY IE AGV S V+S + ++ + Sbjct: 287 AANLLENVRHVQIIACGTSYHAGMVARYWIEELAGVACSV---EVASEFRYRKHVIQQDT 343 Query: 114 LYLAISQSGKSPDLLAAVKAAKAAGAHA-VALVNVVDSPLAALADEVIPLHAGPELSVAA 172 L+L ISQSG++ D LAA++ AK AG A +A+ NV S L +D VI AGPE+ VA+ Sbjct: 344 LFLCISQSGETADTLAALRQAKKAGFRAALAICNVPGSSLVRESDLVIMTQAGPEIGVAS 403 Query: 173 TKSYIAALVAVTQLIAAWT--------EDAELTAALQDLPTALAAAWTLDWSLAV--ERL 222 TK++ L A+ A ++AE+ AL +P ++ LD +A + Sbjct: 404 TKAFTTQLTALLIFTLALARHNGLPEEQEAEIVEALHLVPGQVSDVLALDGEIAEMSKAF 463 Query: 223 KTASNLYVLGRGVGFGVALEAALKFKETCGLHAEAFSAAEVLHGPMALVKDGFPALVFAQ 282 ++ LGRG F VALE ALK KE +HAEA+ A E+ HGP+ALV P + A Sbjct: 464 MDKNHSLFLGRGSQFPVALEGALKLKEISYIHAEAYPAGELKHGPLALVDSEMPVVTVAP 523 Query: 283 NDESRASVDEMAAGLRARGASVLI-AGGGGD--APDALPTL---ASHPVLEPILMIQSFY 336 N++ + +RARG + + A D A + L + + HP+ PI+ Sbjct: 524 NNDLVEKLKSNLEEVRARGGELFVFADKKADVKAEEGLHVMQIPSVHPITAPIVYTVPLQ 583 Query: 337 RMANALSVARGYDPDSPPHLNK 358 ++ ++V +G D D P +L K Sbjct: 584 LLSYHVAVLKGTDVDQPRNLAK 605 Lambda K H 0.315 0.128 0.360 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: 375 Number of extensions: 16 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 363 Length of database: 610 Length adjustment: 33 Effective length of query: 330 Effective length of database: 577 Effective search space: 190410 Effective search space used: 190410 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