Align Glucosamine-6-phosphate deaminase (EC 3.5.99.6) (characterized)
to candidate 349786 BT0258 glucosamine-6-phosphate isomerase (NCBI ptt file)
Query= reanno::Pedo557:CA265_RS21925 (641 letters) >FitnessBrowser__Btheta:349786 Length = 663 Score = 675 bits (1741), Expect = 0.0 Identities = 327/631 (51%), Positives = 438/631 (69%), Gaps = 4/631 (0%) Query: 10 TRFEKLPVSVFENPKIASINVAHRIAELIKSKQANNTPAVLGLATGVTPIAVYAELVRLH 69 TR EK+P ++E+ + + +A IA+ I+ KQ VL L G +P VY+EL+R+H Sbjct: 31 TRLEKIPTDIYESVEEGANYIACEIAQTIREKQKAGRFCVLALPGGNSPSHVYSELIRMH 90 Query: 70 KEEGLSFKNVITFNLDEYYPMAPTAAQSYVTFMNENLFNHIDIDKKNVHIPDGTLALEDI 129 KEEGLSF+NVI FN+ EYYP+ A S + E L +H+DIDK+N+ PDGT+A + I Sbjct: 91 KEEGLSFRNVIVFNMYEYYPLTADAINSNFNALKEMLLDHVDIDKQNIFTPDGTIAKDTI 150 Query: 130 PAFCLEYEKKIGDLGGLDIQILGIGRTGHIGFNEPGSAPNSGTRLVTLDDLTRRDAARDF 189 +C YE++I GG+DI +LGIGR G+I FNEPGS NS TRL+ LD+ +R +A++ F Sbjct: 151 FEYCRLYEQRIESFGGIDIALLGIGRVGNIAFNEPGSRLNSTTRLILLDNASRNEASKIF 210 Query: 190 GGKTFVPTKAITMGIGTIFKAREIILMAWSRKKASIIKKAVEGEISGDVPATFLQLSDHV 249 G P +ITMG+ TI A+++ L+AW KA++IK+ VEG IS +PA++LQ ++ Sbjct: 211 GTIENTPISSITMGVSTILGAKKVYLLAWGENKAAMIKECVEGPISDTIPASYLQTHNNA 270 Query: 250 EFILDAPAASELTRFYTPWLVKDCVWTDALIRKAVIWLANTLKKPILKLTEDDYNNNGMA 309 +D A+ LTR PWLV C W D LIR A++WL KPILKLT DYN NG++ Sbjct: 271 HVAIDLSASMNLTRIQRPWLVTSCEWNDKLIRSAIVWLCQLTGKPILKLTNKDYNENGLS 330 Query: 310 QLATEKGPVYNINIHIFNKLQHTITGWPGGKPNADDSQRPERAEPAKKRVIIFSPHPDDD 369 +L G YN+NI IFN LQHTITGWPGGKPNADD+ RPERA+P KRV+IFSPHPDDD Sbjct: 331 ELLALFGSAYNVNIKIFNDLQHTITGWPGGKPNADDTYRPERAKPYPKRVVIFSPHPDDD 390 Query: 370 VISMGGTFLRLVDQGHDVHVAYQTSGNTAVWDDDALRFVEFNVDFTEKM-GMDNTHLKDL 428 VISMGGT RLV+Q H+VHVAY+TSGN AV D++ +RF+ F F + ++ + + Sbjct: 391 VISMGGTLRRLVEQKHEVHVAYETSGNIAVGDEEVVRFMHFINGFNQIFNNSEDLVISEK 450 Query: 429 YNKMRAFIEQKKPNQIDTPEIQTVKGLIRKGEAIAGARYCGLEDDHIHFQALPFYESGKV 488 Y ++R F+++KK +D+ +I T+KGLIR+GEA + Y + D +HF LPFYE+GK+ Sbjct: 451 YAEIRKFLKEKKDGDMDSRDILTIKGLIRRGEARTASSYNNIPLDRVHFLDLPFYETGKI 510 Query: 489 QKNPVTDADIELTIELLQKVKPQQVYAAGDFEDPHGTHIVCFNIILEALKRLRKTEA--W 546 QKNP+++AD+E+ LL+++KP Q++ AGD DPHGTH VC + + A+ L K E W Sbjct: 511 QKNPISEADVEIVRNLLREIKPHQIFVAGDLADPHGTHRVCTDAVFAAVD-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 QRSEDRNRGTATLYDQLGLASYEAMEAFVEY 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: 1101 Number of extensions: 45 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 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