Align Glyceraldehyde dehydrogenase large chain; Glyceraldehyde dehydrogenase subunit A; Glyceraldehyde dehydrogenase subunit alpha; EC 1.2.99.8 (characterized)
to candidate WP_047216151.1 PATSB16_RS01635 xanthine dehydrogenase family protein molybdopterin-binding subunit
Query= SwissProt::Q4J6M3 (748 letters) >NCBI__GCF_001931675.1:WP_047216151.1 Length = 790 Score = 456 bits (1174), Expect = e-132 Identities = 287/780 (36%), Positives = 424/780 (54%), Gaps = 43/780 (5%) Query: 5 GKSIKRLNDDKFITGRSNYIDDIKIPS-LYAGFVRSPYPHAIIKRIDATDALKVNGIVAV 63 G++++R D +F+TG Y DD+++ YA FVRSPY HA I+ A + G+V + Sbjct: 10 GQAVRRKEDYRFLTGAGQYTDDVQMDGQTYAYFVRSPYAHARIRGYRLDAARQAPGVVGI 69 Query: 64 FSGKDINPMLKGGV--GVLSAYVNPSLFRFKERKAFPEDNKVKYVGEPVAIVIGQDKYAV 121 F+G+DI GG+ G L V+ + D V+YVG+ VA+VI Q Sbjct: 70 FTGEDIKRAGIGGLPCGWLITDVHGQPMKEPPHPVLAIDT-VRYVGDQVALVIAQTLAQA 128 Query: 122 RDAIDRVNVEYEQLKPVIKMEDAEKDEV-IVHDELKTNVSYKIPFKAGD---IEKAFSQA 177 RDA + V+V+YE L V+ + A + VHD NV Y + GD ++ A ++A Sbjct: 129 RDAAELVDVDYEPLDAVVAPDAAVRSGAPAVHDIAPDNVCYV--WSLGDQAAVDAAMAKA 186 Query: 178 DKVVKVEAINERLIPNPMEPRGILSVYD--GNSLSVWYSTQVPHFARSEFAR-IFGIPET 234 V +++ +N RLIPN +EPR ++ Y +S +++ + Q PH R A + +PE Sbjct: 187 AHVTRLDFVNNRLIPNAIEPRAAVAHYSRADDSYTLYVANQNPHVERLLMAAFVLNLPEH 246 Query: 235 KIRVAMPDVGGAFGSKVHIMAEELAVIASSILLRRPVRWTATRSEEMLA-SEARSNVFTG 293 K+RV PDVGG FGSK+ + AEE A++ +S + RP++WTA RSE L+ + R +V T Sbjct: 247 KLRVVAPDVGGGFGSKIFLYAEETALVWASKQINRPIKWTAERSESFLSDAHGRDHVTTA 306 Query: 294 EVAVKKDGTVLGIKGKLLLDLGAYLTLTAGIQPTII-PVMIPGPYKVRDLEIESTAVYTT 352 E+ + +G L ++ +LGAYL+ A PTI+ ++ G Y + E T V+T Sbjct: 307 ELGLDANGKFLALRVHTKANLGAYLSTFASSVPTILYATLLAGQYTTPAIFCEVTGVFTH 366 Query: 353 TPPITMYRGASRPEATYIIERIMSTVADELGLDDVTIRERNLIDQLPYTNPFGLRYDTGD 412 T P+ YRGA RPEATY++ERI+ T A E+ +D V +R RN I Q PY P L YDTG+ Sbjct: 367 TAPVDAYRGAGRPEATYVVERIVETAAREMKIDPVELRRRNFITQFPYQTPVALCYDTGN 426 Query: 413 YIRVFKDGVAKLEYNELRKWAQQERSKGHRVGVGLAFYLEICSFGP-------------W 459 Y + + + R +G G+G + Y+E C P + Sbjct: 427 YGASLDKALQLADVAGFPARREAARQRGKLRGLGYSCYIEACGLAPSNIAGQLGARAGLF 486 Query: 460 EYGEIKVDNKGNVLVITGTTPHGQGTETAIAQIVADALQIPIEKIRVVWGDTDIVEGSFG 519 E GE++V G V V TG+ HGQG ET QIVAD L I E + +V GDT V G Sbjct: 487 EAGEVRVHPTGKVTVFTGSHSHGQGHETTFTQIVADRLGIAYEDVDIVHGDTGRVPFGMG 546 Query: 520 TYGSRSLTIGGSAALKVAERVLDKMKRAAASYFNADVQEIRYENEEFSVKNDPSKKASWD 579 TYGSRSL +GGSA +K ++V+ K K+ AA A +I +++ +FSV K + Sbjct: 547 TYGSRSLAVGGSAIVKALDKVIAKGKKIAAHMLEAAEGDIEFKDGKFSVAG-TDKALPFA 605 Query: 580 EIA---------SLATTKEPIVEKIYYE-NDVTFPYGVHVAVVEVD-DLGMARVVEYRAY 628 +IA L + + + E +Y+ + T+P G H+ VEVD D G +V A Sbjct: 606 QIALSAYVPHNYPLESLEPGLDESAFYDPTNFTYPAGSHICEVEVDPDTGQTEIVAMTAV 665 Query: 629 DDIGKVINPALAEAQIHGGGVQGVGQALYEKAIIN-ENGQ-LSVTYADYYVPTAVEAPRF 686 DD G ++NP + E Q+HGG QG+GQAL E + + E+GQ L+ +Y DY +P A + P F Sbjct: 666 DDFGNIVNPMIVEGQVHGGLAQGIGQALLEGCVYDPESGQLLTGSYMDYAMPRADDLPSF 725 Query: 687 ISYFADKSHPSNYPTGTKGVGEAALIVGPAAIIRAIEDAVGARFTKTPTPPEEIYKAIMS 746 + + ++ P G KG GEA I P A+I AI DA+G + P PE +++A+ + Sbjct: 726 -AVDTTCTPCTHNPLGVKGCGEAGAIGSPPAVINAITDALGVLHLEMPATPERVWRALQT 784 Lambda K H 0.317 0.136 0.390 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: 1409 Number of extensions: 72 Number of successful extensions: 14 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: 748 Length of database: 790 Length adjustment: 41 Effective length of query: 707 Effective length of database: 749 Effective search space: 529543 Effective search space used: 529543 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 (21.6 bits) S2: 55 (25.8 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