Align Glucosamine-6-phosphate deaminase [isomerizing], alternative (EC 3.5.99.6) (characterized)
to candidate WP_009123332.1 BUB52_RS09485 glutamine--fructose-6-phosphate transaminase (isomerizing)
Query= reanno::pseudo3_N2E3:AO353_04455 (336 letters) >NCBI__GCF_900129655.1:WP_009123332.1 Length = 614 Score = 112 bits (281), Expect = 2e-29 Identities = 95/308 (30%), Positives = 152/308 (49%), Gaps = 19/308 (6%) Query: 41 VARGSSDHAASYFAYLTMQHVGIPVASLPMSVVTMQQAPLKVSGQAVFAFSQSGQSPDLV 100 VA G+S HAA +L IPV + + + P+ S V A SQSG++ D + Sbjct: 304 VACGTSWHAALIGKHLIESFCRIPV-EVEYASEFRYRDPVIDSSDVVIAISQSGETADTL 362 Query: 101 NSLRLLRKRGALSISMVNAENSPLEAACEFSLPLCAGTESSVAATKSF---IATLSASAR 157 ++ L + RGA + NA S + A + G E VA+TK+F + L+ A Sbjct: 363 AAIELAKSRGAFIYGICNAIGSSIPRATNTGSYIHVGPEIGVASTKAFTGQVTVLTMLAL 422 Query: 158 LIAYWKQDPELLQAGLAL-------PEGLRDAATQDWSLAV--DVLRDCQRLMVIGRGAG 208 +A K+ + Q LA+ P +++ + +A + + +GRG Sbjct: 423 TLAREKRTIDETQY-LAIVRELGQIPGKMKEVLKLNDRIAELSKIFTYVHNFIYLGRGYS 481 Query: 209 FAIAQEAALKLKETSAIQAEAFSSAEVKHGPMALIDDNYPLLVFAPRGAEQAGLLSLAAE 268 + +A E ALKLKE S I AE + +AE+KHGP+ALID P++V A + +LS E Sbjct: 482 YPVALEGALKLKEISYIHAEGYPAAEMKHGPIALIDAEMPVVVIATQNGLYEKVLSNIQE 541 Query: 269 MRQRGARV--LLAAPDDVSER--DLTLSRAE-HPALDPILAIQSFYVMAAGLAVARGMDP 323 ++ R RV ++ D V + D+ + E L P++ ++A +AV +GMD Sbjct: 542 IKARKGRVIAIVTKGDTVIGKIADICIELPETMECLGPLITTVPLQLLAYHIAVCKGMDV 601 Query: 324 DQPRHLSK 331 D+PR+L+K Sbjct: 602 DRPRNLAK 609 Lambda K H 0.318 0.130 0.362 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: 354 Number of extensions: 15 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: 336 Length of database: 614 Length adjustment: 33 Effective length of query: 303 Effective length of database: 581 Effective search space: 176043 Effective search space used: 176043 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 (21.8 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