Align Glucosamine-6-phosphate deaminase (EC 3.5.99.6) (characterized)
to candidate WP_009120567.1 BUB52_RS12750 glucosamine-6-phosphate deaminase
Query= reanno::Pedo557:CA265_RS21925 (641 letters) >NCBI__GCF_900129655.1:WP_009120567.1 Length = 663 Score = 685 bits (1767), Expect = 0.0 Identities = 329/631 (52%), Positives = 439/631 (69%), Gaps = 4/631 (0%) Query: 10 TRFEKLPVSVFENPKIASINVAHRIAELIKSKQANNTPAVLGLATGVTPIAVYAELVRLH 69 TR EK+P ++E+P+ + +A IA++I+ KQ VL LA G +P VY+ LVR+H Sbjct: 31 TRLEKIPTDIYESPEEGANQIALDIAQVIRDKQKAGRFCVLALAGGNSPRNVYSALVRMH 90 Query: 70 KEEGLSFKNVITFNLDEYYPMAPTAAQSYVTFMNENLFNHIDIDKKNVHIPDGTLALEDI 129 KEEGLSF+NV+ FNL EYYP+A A S + + E L +H+DID +NV P+GT+A + I Sbjct: 91 KEEGLSFRNVVVFNLYEYYPLASDAVNSNLNALKEMLLDHVDIDMQNVFSPNGTIAKDTI 150 Query: 130 PAFCLEYEKKIGDLGGLDIQILGIGRTGHIGFNEPGSAPNSGTRLVTLDDLTRRDAARDF 189 +C YE++I GG+D+ +LGIGR G+IGFNEPGS NS TRL+ LD +R +A++ F Sbjct: 151 FEYCRLYEQRIESFGGIDVAVLGIGRVGNIGFNEPGSRLNSTTRLILLDSDSRNEASKMF 210 Query: 190 GGKTFVPTKAITMGIGTIFKAREIILMAWSRKKASIIKKAVEGEISGDVPATFLQLSDHV 249 G P +ITMG+ TI A+++ L+AW +KA ++K+ VEG ++ +PA++LQ ++ Sbjct: 211 GSIESTPVSSITMGVATILSAKKVYLLAWGEEKAKMVKECVEGNVTDTIPASYLQTHNNA 270 Query: 250 EFILDAPAASELTRFYTPWLVKDCVWTDALIRKAVIWLANTLKKPILKLTEDDYNNNGMA 309 +D AA+ LTR PWLV C W D LIR A++WL KPILKLT DYN NG++ Sbjct: 271 HIAIDLSAAANLTRIQRPWLVTSCEWNDKLIRSAIVWLCQLTGKPILKLTNKDYNENGLS 330 Query: 310 QLATEKGPVYNINIHIFNKLQHTITGWPGGKPNADDSQRPERAEPAKKRVIIFSPHPDDD 369 +L G YN+NI IFN LQHTITGWPGGKPNADD+ RPERA+P KRV++FSPHPDDD Sbjct: 331 ELLALYGSAYNVNIKIFNDLQHTITGWPGGKPNADDTYRPERAKPYPKRVVVFSPHPDDD 390 Query: 370 VISMGGTFLRLVDQGHDVHVAYQTSGNTAVWDDDALRFVEFNVDFTEKM-GMDNTHLKDL 428 VISMGGT RLV+Q HDVHVAY+TSGN AV D++ +RF+ F F + ++ + + Sbjct: 391 VISMGGTIRRLVEQKHDVHVAYETSGNIAVGDEEVIRFLHFINGFNQLFNNSEDQVINEK 450 Query: 429 YNKMRAFIEQKKPNQIDTPEIQTVKGLIRKGEAIAGARYCGLEDDHIHFQALPFYESGKV 488 Y ++R +++ KK +DT +I T+KGLIR+GEA Y + DH HF LPFYE+GK+ Sbjct: 451 YTEIRNYLKDKKDGDMDTRDILTIKGLIRRGEARTACTYNNIPLDHCHFLDLPFYETGKI 510 Query: 489 QKNPVTDADIELTIELLQKVKPQQVYAAGDFEDPHGTHIVCFNIILEALKRLRKTEA--W 546 QKNP+++AD+E+ LL++VKP Q++ AGD DPHGTH VC + + A+ L K E W Sbjct: 511 QKNPISEADVEIVRNLLREVKPHQIFVAGDLADPHGTHRVCTDAVFAAID-LEKEEGAKW 569 Query: 547 AQDCWLWMYRGAWHEFETHEIEMAVPISPQELERKKYAIFKHQSQKDRAVFPGDDSREFW 606 +DC +WMYRGAW E+E IEMAVPISP+EL K+ +I KHQSQ + A F G+D R FW Sbjct: 570 LKDCRIWMYRGAWAEWEIENIEMAVPISPEELRAKRNSILKHQSQMESAPFLGNDERLFW 629 Query: 607 QRAEDRNRDTAKAYDELGLAEYEAMEAFVRW 637 QR+EDRNR TA YD LGLA YEAMEAFV + Sbjct: 630 QRSEDRNRGTAALYDSLGLASYEAMEAFVEY 660 Lambda K H 0.319 0.136 0.412 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: 1074 Number of extensions: 44 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: 641 Length of database: 663 Length adjustment: 38 Effective length of query: 603 Effective length of database: 625 Effective search space: 376875 Effective search space used: 376875 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 54 (25.4 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