Align Glucosamine-6-phosphate deaminase [isomerizing], alternative (EC 3.5.99.6) (characterized)
to candidate WP_011651952.1 RL_RS12290 glutamine--fructose-6-phosphate transaminase (isomerizing)
Query= reanno::pseudo3_N2E3:AO353_04455 (336 letters) >NCBI__GCF_000009265.1:WP_011651952.1 Length = 608 Score = 122 bits (306), Expect = 2e-32 Identities = 92/302 (30%), Positives = 149/302 (49%), Gaps = 33/302 (10%) Query: 55 YLTMQHVGIPVASLPMSVVTMQQAPLKVSGQAVFAFSQSGQSPDLVNSLRLLRKRGALSI 114 Y ++ +PV S ++ PL S A+F SQSG++ D + LR R G Sbjct: 310 YWFERYARLPVEIDVASEFRYREMPLSPSQAALF-ISQSGETADTLACLRYCRDNGLKIG 368 Query: 115 SMVNAENSPLEAACEFSLPLCAGTESSVAATKSF---IATLSASA--------------- 156 ++VN S + + P+ AG E VA+TK+F +A L+A A Sbjct: 369 AVVNVRESTIARESDAVFPIMAGPEIGVASTKAFTCQLAVLAALAIGAGKARGTVSADEE 428 Query: 157 -RLIAYWKQDPELLQAGLALPEGLRDAATQDWSLAVDVLRDCQRLMVIGRGAGFAIAQEA 215 L+ + + P ++ L L + ++ +++ L C+ ++ +GRG F +A E Sbjct: 429 RALVRHLAEMPRIMSRVLNLIQPQMESLSRE-------LSKCKDVLYLGRGTSFPLAMEG 481 Query: 216 ALKLKETSAIQAEAFSSAEVKHGPMALIDDNYPLLVFAPRGAEQAGLLSLAAEMRQRGAR 275 ALKLKE S I AE +++ E+KHGP+ALID+N P++V AP +S E+ RG R Sbjct: 482 ALKLKEISYIHAEGYAAGELKHGPIALIDENMPVIVIAPYDRFFEKTVSNMQEVAARGGR 541 Query: 276 VLLAAPD--DVSERDLTLSRAEHPALDPILAIQSF----YVMAAGLAVARGMDPDQPRHL 329 ++ + + + T++ P +D I+A F ++A AV G D DQPR+L Sbjct: 542 IIFITDEAGAAASKLPTMATITLPVVDEIIAPMIFSLPIQLLAYHTAVFMGTDVDQPRNL 601 Query: 330 SK 331 +K Sbjct: 602 AK 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: 399 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: 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 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