Align Glucosamine-6-phosphate deaminase [isomerizing], alternative (EC 3.5.99.6) (characterized)
to candidate WP_059150433.1 V474_RS05345 glutamine--fructose-6-phosphate transaminase (isomerizing)
Query= reanno::Korea:Ga0059261_1644 (347 letters) >NCBI__GCF_001046635.1:WP_059150433.1 Length = 607 Score = 163 bits (413), Expect = 1e-44 Identities = 124/356 (34%), Positives = 175/356 (49%), Gaps = 32/356 (8%) Query: 14 MEREAAEAGAAVSRMLAANRDAIERVAAR------LRASPPAVVVTCARGSSDHAATYAK 67 M++E E V++ L + +++ A L A +V C G+S +A AK Sbjct: 252 MQKEIFEQPTVVAQTLRSYLRQVDQSVALPQIDFDLGAINRITIVAC--GTSYYAGMVAK 309 Query: 68 YLIETLTGVPTASAALSVAS--LYDAPVAPGNGLCLAISQSGKSPDLLATVEHQRKAGAF 125 Y IET +P + VAS Y PV GL L ISQSG++ D LA + H + AG Sbjct: 310 YWIETFARLPVD---IDVASEFRYRDPVLEAGGLALFISQSGETADTLAALRHCKAAGQT 366 Query: 126 VVAMVNAEDSPLAALADIVIPLKAGPERSVAATKSYICSLAAIAALVAAWA-----QDEA 180 + +VN S +A AD+++P AGPE VA+TK++ C LA +AAL A A D A Sbjct: 367 IAVVVNVPTSTMAREADLLLPTHAGPEIGVASTKAFTCQLAVLAALAAHLAVKRGRMDRA 426 Query: 181 LETAVA----DLPAQLERAFALDWSAAVTA--LTGASGLFVLGRGYGYGIAQEAALKFKE 234 E V PA L A D A A + A + LGRG Y +A E ALK KE Sbjct: 427 EEMEVVHHLLQTPASLNAALDHDEEIAAMAHLIAPARDVLYLGRGPDYPLALEGALKLKE 486 Query: 235 TCALHAESFSAAEVRHGPMAIVGEAFHVLAFASSDRAGESVRETVAEFRSRGAEVLLADP 294 +HAE +++ E++HGP+A++ EA V+ A S E + E R+RG +V+L Sbjct: 487 ISYIHAEGYASGEMKHGPIALIDEAVPVIVLAPSGPLFEKTVSNMQEVRARGGKVVLISD 546 Query: 295 A--ARQAGLPAIA------AHPAIEPILIVQSFYKMANALALARGCDPDSPPHLNK 342 A +AG IA HP I P++ +A +A +G D D P +L K Sbjct: 547 AEGIAEAGEGCIATIEMPRVHPLIAPLVYAVPVQLLAYHVACVKGTDVDQPRNLAK 602 Lambda K H 0.317 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: 454 Number of extensions: 20 Number of successful extensions: 4 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: 347 Length of database: 607 Length adjustment: 33 Effective length of query: 314 Effective length of database: 574 Effective search space: 180236 Effective search space used: 180236 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 (21.7 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