Align glycolaldehyde oxidoreductase large subunit (characterized)
to candidate WP_011386063.1 AMB_RS18770 xanthine dehydrogenase family protein molybdopterin-binding subunit
Query= metacyc::MONOMER-18071 (749 letters) >NCBI__GCF_000009985.1:WP_011386063.1 Length = 732 Score = 360 bits (924), Expect = e-103 Identities = 242/756 (32%), Positives = 371/756 (49%), Gaps = 44/756 (5%) Query: 5 GKPVKRIYDDKFVTGRSTYVDDIRIPAL-YAGFVRSTYPHAIIKRIDVSDALKVNGIVAV 63 G+ R+ D +F+TG Y DDI + Y VRS PHA + +D A + G++ V Sbjct: 7 GQSRTRVEDLRFLTGGGCYTDDINLTGQSYGMVVRSLLPHADVT-VDAVAARAMPGVLLV 65 Query: 64 FTAKEINPLLKGGIRPWPT-YIDIRSFRYSERKAFPENKVKYVGEPVAIVLGQDKYSVRD 122 TA E + + GI P ++ + R + ++ GEP+A V+ + RD Sbjct: 66 LTAAE---MAEQGIGPMVCGFLPEDAVPRHPRPVIAGPRTRHAGEPLAFVVAETLAQARD 122 Query: 123 AIDKVVVEYEPLKPVIRMEEAEKDQVIIHEELKTNISYKIPFKAGEVDKAFSESDKVVRV 182 A + V+V+Y PL H+ + A V +AF+ + +VV + Sbjct: 123 AAEAVLVDYHPLPATP------------HDAFVWEMG-----DASRVAEAFARAARVVEL 165 Query: 183 EAINERLIPNPMEPRGIVSR-FEAGTLSIWYSTQVPHYMRSEFARILGIPESKIKVSMPD 241 + IN RL P MEPR ++R G L + +Q H +R A +LGI ++ V PD Sbjct: 166 DLINNRLAPTAMEPRACLARPLPGGRLELTAGSQGVHEIRDRLAPVLGIAADRLDVITPD 225 Query: 242 VGGAFGAKVHLMPEELAVVASSIILGRPVRWTATRSEEMLA-SEARHNVFTGEVAVKRDG 300 VGG FG K+ PE+ + ++ IL RPV+WT R+E L+ + R ++ T +A+ +G Sbjct: 226 VGGGFGLKISPFPEQAMALVAARILDRPVKWTGDRTESFLSDTHGRGHLSTARLALDAEG 285 Query: 301 TILGIKGKLLLDLGAYITVTAGIQPLIIPM-MIPGPYKIRNLDIESVAVYTNTPPITMYR 359 LG++ + + DLGAYI+ P + M+ G Y I A++T+T P+ YR Sbjct: 286 RFLGLQVETVADLGAYISNYGAFVPTLAGTGMLTGVYDIPAFHARVRAIHTHTTPVDAYR 345 Query: 360 GASRPEATYIIERIMSTVADELGLDDVSIREKNLVTE--LPYTNPFGLRYDSGDYVGLLR 417 GA RPEA Y IER++ A + GL V IR++N + PY + YDSG++ ++ Sbjct: 346 GAGRPEAAYCIERLVDAAAHDTGLSPVEIRKRNFIPPDAFPYASAGRHTYDSGEFARVMD 405 Query: 418 EGVKRLGYYELKKWAEEERKKGHRVGVGLAYYLEICSFGPWEYAEVRVDERGDVLVVTGT 477 ++R G+ + + +G + G+GLAYY+EIC E + + G ++ GT Sbjct: 406 RALERSGWADFASRQADSTARGRKRGIGLAYYIEICGGTSGEDVTLTLSPDGGAEILVGT 465 Query: 478 TPHGQGTETAIAQIVADALQIDISRVRVIWGDTDTVAASMGTYGSRSVTIGGSAAIKVAE 537 +GQG ETA AQ+VA L + I RVRVI GDT + GT GSRS++ G A E Sbjct: 466 QSNGQGHETAYAQMVAAELGLAIERVRVIQGDTRRIGTGGGTGGSRSLSQQGGAIASAVE 525 Query: 538 KILDKMKRIAASTWNVDVQEVQYEKGEFKLKNDPSKKMSWDDVASIAYRSHDPGLVEKII 597 ++ ++ AA + + +++ G ++ A + + P Sbjct: 526 SFIEHLQPQAARL--LQAERAEFDAGFYRAAGGSV------SFAQVLAEAETPLAASLRF 577 Query: 598 YENDVTFPYGVHIATVEVD-DTGVARVLEYRAYDDIGKVVNPALAEAQIHGGGVQAVGQA 656 TFP G H+ VEVD +TG ++ Y DD+G V+NP L + QI GG VQ +GQA Sbjct: 578 RPPAATFPNGCHVCEVEVDPETGETEIVRYTIVDDVGTVLNPLLLKGQIVGGAVQGIGQA 637 Query: 657 LYEQALLNENG--QLIVTYADYYVPTAVEAPK--FTSVFADQYHPSNYPTGSKGVGEAAL 712 L E A+ + L + DY VP A P+ F++V + +P G KG GEA Sbjct: 638 LLEHAVFDPESTQPLTSSLIDYAVPRAAHIPEIDFSTV---EIPCRTHPLGLKGAGEAGT 694 Query: 713 IVGPAVIIRALEDAIGTRFTKTPTTPEEILRAIASK 748 I +I AL +A+ R P TP + A+ K Sbjct: 695 IGAAPAVINALCNALELRHMDMPATPLAVWNALNGK 730 Lambda K H 0.317 0.136 0.394 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: 1279 Number of extensions: 71 Number of successful extensions: 9 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: 749 Length of database: 732 Length adjustment: 40 Effective length of query: 709 Effective length of database: 692 Effective search space: 490628 Effective search space used: 490628 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: 55 (25.8 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