Align Glucosamine-6-phosphate deaminase [isomerizing], alternative (EC 3.5.99.6) (characterized)
to candidate SMc00231 SMc00231 glucosamine--fructose-6-phosphate aminotransferase
Query= reanno::pseudo3_N2E3:AO353_04455 (336 letters) >FitnessBrowser__Smeli:SMc00231 Length = 608 Score = 125 bits (313), Expect = 4e-33 Identities = 100/317 (31%), Positives = 160/317 (50%), Gaps = 24/317 (7%) Query: 35 PQVAMTVARGSSDHAASYFAYLTMQHVGIPVASLPMSVVTMQQAPLKVSGQAVFAFSQSG 94 P +A++ A G++ A Y ++ +PV S ++ PL A+F SQSG Sbjct: 291 PSLAIS-ACGTAYLAGLIGKYWFERYARLPVEIDVASEFRYREIPLSPQSAALF-ISQSG 348 Query: 95 QSPDLVNSLRLLRKRGALSISMVNAENSPLEAACEFSLPLCAGTESSVAATKSFIATLSA 154 ++ D + SLR ++ G ++VNA S + + P+ AG E VA+TK+F L+ Sbjct: 349 ETADTLASLRYCKEHGLKIGAVVNARESTIARESDAVFPILAGPEIGVASTKAFTCQLAV 408 Query: 155 SARLIA---------YWKQDPELLQAGLALP----EGLRDAATQDWSLAVDVLRDCQRLM 201 A L +++ L+++ +P + L + SL+ + L C ++ Sbjct: 409 LAALAVGAGKARGTISGEEEQALVKSLAEMPRIMGQVLNSIQPKIESLSRE-LSKCHDVL 467 Query: 202 VIGRGAGFAIAQEAALKLKETSAIQAEAFSSAEVKHGPMALIDDNYPLLVFAPRGAEQAG 261 +GRG F +A E ALKLKE S I AE +++ E+KHGP+ALID+N P++V AP Sbjct: 468 YLGRGTSFPLAMEGALKLKEISYIHAEGYAAGELKHGPIALIDENMPVIVIAPHDRFFDK 527 Query: 262 LLSLAAEMRQRGARVLLAAPDD---VSERDLTLSRAEHPALDPILAIQSF----YVMAAG 314 +S E+ RG R++L + S+ D T+ P +D I+A F ++A Sbjct: 528 TVSNMQEVAARGGRIILITDEKGAAASKLD-TMHTIVLPEVDEIIAPMIFSLPVQLLAYH 586 Query: 315 LAVARGMDPDQPRHLSK 331 AV G D DQPR+L+K Sbjct: 587 TAVFMGTDVDQPRNLAK 603 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: 424 Number of extensions: 19 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: 608 Length adjustment: 33 Effective length of query: 303 Effective length of database: 575 Effective search space: 174225 Effective search space used: 174225 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 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