Align Glucosamine-6-phosphate deaminase [isomerizing], alternative (EC 3.5.99.6) (characterized)
to candidate WP_075619473.1 GY23_RS12080 glutamine--fructose-6-phosphate transaminase (isomerizing)
Query= reanno::Phaeo:GFF2746 (342 letters) >NCBI__GCF_001939075.1:WP_075619473.1 Length = 600 Score = 124 bits (310), Expect = 8e-33 Identities = 108/363 (29%), Positives = 172/363 (47%), Gaps = 33/363 (9%) Query: 1 MTDITK------MRREIDEIPTAVDRLLS---HGRVEIEAVADAARAL-DPNVMVTVARG 50 M+DI K M +EIDE P + +++ + + E+E D AL + + + +A G Sbjct: 240 MSDIEKGTYPHYMLKEIDEQPGVMRKIIQAYQNEQGELEIDQDIITALNEADRLYIIAAG 299 Query: 51 SSDHVCTYLKYASEIMLGVPVASVGPSVASIYKAPLRLKGALSLAVSQSGKSPDIVSMAG 110 +S H K E + G+PV V S Y PL K L L ++QSG++ D + Sbjct: 300 TSYHAGLVGKEYFEKIAGIPV-EVHISSEFGYNMPLLSKKPLFLFITQSGETADSRQVLV 358 Query: 111 SARKDGALSVALTNDAASPLAAAADHTLDIHAGPELSVAATKTF--------VTSAVAG- 161 +K G ++ LTN S L+ ADHTL +HAGPE++VA+TK + +T+AVA Sbjct: 359 KIKKLGHPTLTLTNAKGSTLSREADHTLLLHAGPEIAVASTKAYTAQIAVLAITAAVAAE 418 Query: 162 -LWLLAQWDRNQAVLAALHALPEQLDRACRIDWPEVRDAIGARSSLFTLGRGQALAVSNE 220 A +D + +A+ +D +++ D + + F +GR VS E Sbjct: 419 KAGRKADFDIVHEMSIVANAVQSLVDSKEKME-QIATDFLSTTRNAFFIGRNLDFCVSME 477 Query: 221 AALKFKETCQLHAESYSSAEVLHGPVSIVEEGFPVLGFAAADAAEGALAGIADQIAAKGA 280 ALK KE + AE ++ E+ HG ++++EEG P+ A A + G ++ A+GA Sbjct: 478 GALKLKEISYIQAEGFAGGELKHGTIALIEEGTPIFALATQKAVSLNIRGNVKEVVARGA 537 Query: 281 Q--VFATTDKVTAARRVDHVRTDHALTDPISLI----VSFYAMVEAFAASRGIDPDAPRH 334 + A + LT +S+I +S+YA + RG D D PR+ Sbjct: 538 NPCIIAMEGMEEEGDTLVLPNVHPLLTPLVSVIPLQLISYYASLH-----RGCDVDKPRN 592 Query: 335 LKK 337 L K Sbjct: 593 LAK 595 Lambda K H 0.317 0.129 0.364 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: 305 Number of extensions: 11 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: 342 Length of database: 600 Length adjustment: 33 Effective length of query: 309 Effective length of database: 567 Effective search space: 175203 Effective search space used: 175203 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