Align Glucosamine-6-phosphate deaminase [isomerizing], alternative (EC 3.5.99.6) (characterized)
to candidate 5211430 Shew_3839 glucosamine--fructose-6-phosphate aminotransferase, isomerizing (RefSeq)
Query= reanno::Caulo:CCNA_00453 (363 letters) >FitnessBrowser__PV4:5211430 Length = 609 Score = 125 bits (315), Expect = 2e-33 Identities = 95/312 (30%), Positives = 150/312 (48%), Gaps = 24/312 (7%) Query: 66 VVTCARGSSDHAATFARYLIETKAGVLTSSAGPSVSSV--YDASPNLEGALYLAISQSGK 123 ++ C G+S HA ARY +E AGV S ++S Y S +L + ISQSG+ Sbjct: 298 IIAC--GTSYHAGMAARYWLEDWAGV---SCNVEIASEFRYRKSHLFPNSLLVTISQSGE 352 Query: 124 SPDLLAAVKAAKAAGAHA-VALVNVVDSPLAALADEVIPLHAGPELSVAATKSYIAALVA 182 + D LAA++ AK G A + + N S L +D + AG E+ VA+TK++ L Sbjct: 353 TADTLAALRLAKEMGYKATLTICNAPGSSLVRESDMAYMMKAGAEIGVASTKAFTVQLAG 412 Query: 183 VTQLIAAWTED--------AELTAALQDLPTALAAAWTLDWSLA--VERLKTASNLYVLG 232 + L AA AE+T +LQ +P + A LD ++A E + LG Sbjct: 413 LLMLTAAVGRHNGMSPEMLAEITQSLQSMPAKVEQALGLDDAIAELAEDFADKHHALFLG 472 Query: 233 RGVGFGVALEAALKFKETCGLHAEAFSAAEVLHGPMALVKDGFPALVFAQNDESRASVDE 292 RG + +A+E ALK KE +HAEA+++ E+ HGP+AL+ P +V A N+E + Sbjct: 473 RGDQYPIAMEGALKLKEISYIHAEAYASGELKHGPLALIDADMPVIVVAPNNELLEKLKS 532 Query: 293 MAAGLRARGASVLIAGG------GGDAPDALPTLASHPVLEPILMIQSFYRMANALSVAR 346 +RARG + + D +P + P++ ++ +++ + Sbjct: 533 NVEEVRARGGLMYVFADKDAEFESDDTMKVIPVPHCDDYMAPLIYTIPLQLLSYHVALIK 592 Query: 347 GYDPDSPPHLNK 358 G D D P +L K Sbjct: 593 GTDVDQPRNLAK 604 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: 345 Number of extensions: 13 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: 363 Length of database: 609 Length adjustment: 33 Effective length of query: 330 Effective length of database: 576 Effective search space: 190080 Effective search space used: 190080 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