Align Glyceraldehyde dehydrogenase large chain; Glyceraldehyde dehydrogenase subunit A; Glyceraldehyde dehydrogenase subunit alpha; EC 1.2.99.8 (characterized)
to candidate BPHYT_RS01765 BPHYT_RS01765 carbon-monoxide dehydrogenase
Query= SwissProt::Q4J6M3 (748 letters) >FitnessBrowser__BFirm:BPHYT_RS01765 Length = 793 Score = 466 bits (1200), Expect = e-135 Identities = 287/789 (36%), Positives = 428/789 (54%), Gaps = 53/789 (6%) Query: 5 GKSIKRLNDDKFITGRSNYIDDIKIPS-LYAGFVRSPYPHAIIKRIDATDALKVNGIVAV 63 G S++R D +F+TG Y DDI +P YA F+RSP+ HA I ID A + G+VA+ Sbjct: 10 GASVERKEDYRFLTGNGQYTDDIVLPQQTYAIFLRSPHAHAKINSIDTAAAKQSPGVVAI 69 Query: 64 FSGKDINPMLKGGVGVLSAYVNPSLFRFKERKAFPED-------NKVKYVGEPVAIVIGQ 116 F+G D M VG L L + K E KV++VG+ VA+VI Sbjct: 70 FTGAD---MAADNVGGLPC---GWLIHSTDGKPMNEPPHPIIAHTKVRHVGDQVALVIAD 123 Query: 117 DKYAVRDAIDRVNVEYEQLKPVIKMEDA-EKDEVIVHDELKTNVSYKIPFKAGD---IEK 172 A +DA + + V+Y+ L V+ A + + VHDE+ N+ Y + GD + Sbjct: 124 SIKAAKDAAELIEVDYDVLPAVVDTAHAADAGQPAVHDEVPDNICYN--WGHGDKAATDA 181 Query: 173 AFSQADKVVKVEAINERLIPNPMEPRGILSVYD--GNSLSVWYSTQVPHFARSEFAR-IF 229 AF++A V ++ +N RL+PN +EPR + + Y +S +++ + Q PH R A + Sbjct: 182 AFAKAAHVTTLDIVNNRLVPNAIEPRAVNASYSVQDDSYTLYVANQNPHVERLLMAAFVL 241 Query: 230 GIPETKIRVAMPDVGGAFGSKVHIMAEELAVIASSILLRRPVRWTATRSEEMLA-SEARS 288 +PE+K+RV PDVGG FGSK+ + AE++A+ +S +RRPV+WTA RSE ++ + R Sbjct: 242 SLPESKLRVIAPDVGGGFGSKIFLYAEDVALTWASKKIRRPVKWTAERSEAFVSDAHGRD 301 Query: 289 NVFTGEVAVKKDGTVLGIKGKLLLDLGAYLTLTAGIQPTII-PVMIPGPYKVRDLEIEST 347 +V E+A+ DG LG++ ++GAYL+ A PTI+ ++ G Y + E Sbjct: 302 HVTKAELAMDADGKFLGMRIHTTANMGAYLSTFASSVPTILYATLLAGQYATPAIYAEVK 361 Query: 348 AVYTTTPPITMYRGASRPEATYIIERIMSTVADELGLDDVTIRERNLIDQLPYTNPFGLR 407 AV+T T P+ YRGA RPEATY++ER++ T A ++ LD IR RN I + PY P GL Sbjct: 362 AVFTNTVPVDAYRGAGRPEATYVVERLVETAARDMKLDPAEIRRRNFIREFPYATPVGLT 421 Query: 408 YDTGDYIRVFKDGVAKLEYNELRKWAQQERSKGHRVGVGLAFYLEICSFGP--------- 458 YDTGDY + + + Q+ G G+G + Y+E C P Sbjct: 422 YDTGDYETILARSLELADVKGFAARKQESEKNGKLRGLGYSCYIEACGLAPSNIAGALGA 481 Query: 459 ----WEYGEIKVDNKGNVLVITGTTPHGQGTETAIAQIVADALQIPIEKIRVVWGDTDIV 514 +E G+I+V G+V V TG+ HGQG ET AQ+VAD L I +E + +V GDT + Sbjct: 482 RAGLFEVGQIRVHPTGSVTVFTGSHSHGQGHETTFAQVVADRLGIALESVEIVHGDTGRI 541 Query: 515 EGSFGTYGSRSLTIGGSAALKVAERVLDKMKRAAASYFNADVQEIRYENEEFSVKNDPSK 574 GTYGSRS+ +GGSA +K +++ K K+ AA A ++I +++ F V Sbjct: 542 PFGMGTYGSRSIAVGGSAIMKALDKIETKAKKIAAHLLEAAAEDIEFKDGVFRVAGTDRT 601 Query: 575 KASWD-EIASLATTKEP-------IVEKIYYE-NDVTFPYGVHVAVVEVD-DLGMARVVE 624 KA D +A+ P + E +Y+ + T+P G ++ +EVD + G+ R+ + Sbjct: 602 KAFADISLAAYVPHNYPLDVLEPGLEESAFYDPTNFTYPSGAYICEIEVDPETGVCRIQQ 661 Query: 625 YRAYDDIGKVINPALAEAQIHGGGVQGVGQALYEKAII-NENGQ-LSVTYADYYVPTAVE 682 + A DD G VINP + E Q+HGG QG+GQA+ E+ + NE+GQ LS +Y DY +P A + Sbjct: 662 FTAVDDFGNVINPMIVEGQVHGGLAQGIGQAMLERCVYDNESGQLLSGSYMDYAMPHASD 721 Query: 683 APRFISYFADKSHPSNYPTGTKGVGEAALIVGPAAIIRAIEDA---VGARFTKTPTPPEE 739 P F + ++ P G KG GEA I P A+I AI DA +G + P P Sbjct: 722 LPNFTVETVKGTPCTHNPLGVKGCGEAGAIGSPPAVINAILDALAPLGVTDLQMPATPHR 781 Query: 740 IYKAIMSKK 748 ++ AI + K Sbjct: 782 VWSAIHAAK 790 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: 1380 Number of extensions: 62 Number of successful extensions: 11 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: 793 Length adjustment: 41 Effective length of query: 707 Effective length of database: 752 Effective search space: 531664 Effective search space used: 531664 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