Align Glyceraldehyde dehydrogenase large chain; Glyceraldehyde dehydrogenase subunit A; Glyceraldehyde dehydrogenase subunit alpha; EC 1.2.99.8 (characterized)
to candidate Ac3H11_3591 Carbon-monoxide dehydrogenase form II, large subunit (EC 1.2.99.2)
Query= SwissProt::Q4J6M3 (748 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3591 Length = 795 Score = 442 bits (1138), Expect = e-128 Identities = 281/790 (35%), Positives = 423/790 (53%), Gaps = 46/790 (5%) Query: 1 MTYTGKSIKRLNDDKFITGRSNYIDDIKIPS-LYAGFVRSPYPHAIIKRIDATDALKVNG 59 + + G+S+KR D +F+TG Y DD+ + + +A FVRSP+ HA I I+ + A G Sbjct: 9 LPHIGESLKRKEDYRFLTGAGQYTDDVVLAAQCHAVFVRSPHAHAGINSINTSAAKAAPG 68 Query: 60 IVAVFSGKDINPMLKGGV--GVLSAYVNPSLFRFKERKAFPEDNKVKYVGEPVAIVIGQD 117 ++ VF G D+ G+ G L N + + KV+YVG+ VA+V+ Q Sbjct: 69 VLGVFVGADVAADNINGLPCGWLITSTNGEPMKEPPHPILAQ-GKVRYVGDHVAMVVAQT 127 Query: 118 KYAVRDAIDRVNVEYEQLKPVIKMEDAEKDEVI---VHDELKTNVSYKIPF-KAGDIEKA 173 RDA + V V+Y+ L V+ + DA V +HD N +K G ++ A Sbjct: 128 LQQARDAAELVEVDYDVLPAVVNVADAAAGAVAGAALHDIAPDNHCFKWAIGDKGAVDAA 187 Query: 174 FSQADKVVKVEAINERLIPNPMEPRGILSVYD--GNSLSVWYSTQVPHFARSEF-ARIFG 230 F+ A V +++ IN RLIPN MEPR + Y + +++ S Q PH R A + G Sbjct: 188 FAGAAHVTQLDLINNRLIPNAMEPRAAIGSYSRANDEYTLYVSNQNPHVERLLMTAFVMG 247 Query: 231 IPETKIRVAMPDVGGAFGSKVHIMAEELAVIASSILLRRPVRWTATRSEEMLA-SEARSN 289 +PE K+RV PDVGG FGSK+++ AE++ + ++ L R ++W A RSE L+ + R + Sbjct: 248 LPEHKVRVIAPDVGGGFGSKIYLYAEDVCLTWAAKKLNRNIKWVADRSESFLSDAHGRDH 307 Query: 290 VFTGEVAVKKDGTVLGIKGKLLLDLGAYLTLTAGIQPTII-PVMIPGPYKVRDLEIESTA 348 + E+A+ KDG L ++ +LGAYL+ A PTI+ ++ G Y + +E + Sbjct: 308 ISHAEMAMDKDGKFLAMRVHTHANLGAYLSTFASAVPTILYATLLAGQYTTPQVYVEVDS 367 Query: 349 VYTTTPPITMYRGASRPEATYIIERIMSTVADELGLDDVTIRERNLIDQLPYTNPFGLRY 408 +T T P+ YRGA RPEATY++ER+++ A ELGL IR+RN I PY P L+Y Sbjct: 368 WFTNTAPVDAYRGAGRPEATYLLERLVTRCAWELGLSQDEIRKRNFITSFPYQTPVALQY 427 Query: 409 DTGDYIRVFKDGVAKLEYNELRKWAQQERSKGHRVGVGLAFYLEICSFGP---------- 458 D GDY + +KG + G+G + Y+E C P Sbjct: 428 DIGDYHACMTQAQQLADVAGFAARKAASEAKGFKRGIGYSSYIEACGIAPSNIAGALGAR 487 Query: 459 ---WEYGEIKVDNKGNVLVITGTTPHGQGTETAIAQIVADALQIPIEKIRVVWGDTDIVE 515 +E GE++V G+V V TG+ HGQG ET AQ+VA L IP+E + +V GDT V Sbjct: 488 AGLFECGEVRVHPTGSVTVFTGSHSHGQGHETTFAQVVAARLGIPVENVDIVHGDTGRVP 547 Query: 516 GSFGTYGSRSLTIGGSAALKVAERVLDKMKRAAASYFNADVQEIRYENEEFSVKNDPSKK 575 GTYGSRS+++GG+A +K +++ K K+ AA A +I + EF+V+ KK Sbjct: 548 FGMGTYGSRSISVGGAAIMKALDKIEAKAKKIAAHLMEASDADIDFSGGEFTVRG-TDKK 606 Query: 576 ASWDEIASLATTK--------EP-IVEKIYYE-NDVTFPYGVHVAVVEVDD-LGMARVVE 624 + ++A A EP + E +Y+ + TFP G ++ VE+D G RV + Sbjct: 607 IPFGQVALTAYVPHNYPLDKLEPGLNETAFYDPTNFTFPAGTYICEVEIDPATGSTRVDK 666 Query: 625 YRAYDDIGKVINPALAEAQIHGGGVQGVGQALYEKAIIN-ENGQ-LSVTYADYYVPTAVE 682 + A DD G +INP + E Q+HGG VQG+GQA+ E + + E GQ L+ ++ DY +P A + Sbjct: 667 FTAVDDFGTIINPMIVEGQVHGGLVQGIGQAVLENCVYDRETGQLLTGSFMDYAMPRADD 726 Query: 683 APRF-ISYFADKSHPSNYPTGTKGVGEAALIVGPAAIIRAIEDA---VGARFTKTPTPPE 738 P F + + ++ P GTKG GEA I P A+I A+ DA +G + P P Sbjct: 727 FPEFKLGHVCTPC--THNPLGTKGCGEAGAIGSPPAVINAVLDALRPLGVKDFDMPASPH 784 Query: 739 EIYKAIMSKK 748 +++AI S K Sbjct: 785 RVWEAIQSAK 794 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: 1355 Number of extensions: 73 Number of successful extensions: 13 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: 795 Length adjustment: 41 Effective length of query: 707 Effective length of database: 754 Effective search space: 533078 Effective search space used: 533078 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 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