Align glycolaldehyde oxidoreductase large subunit (characterized)
to candidate 3610816 Dshi_4202 Carbon-monoxide dehydrogenase (acceptor) (RefSeq)
Query= metacyc::MONOMER-18071 (749 letters) >FitnessBrowser__Dino:3610816 Length = 793 Score = 375 bits (963), Expect = e-108 Identities = 250/781 (32%), Positives = 396/781 (50%), Gaps = 42/781 (5%) Query: 2 SYVGKPVKRIYDDKFVTGRSTYVDDIRIPAL-YAGFVRSTYPHAIIKRIDVSDALKVNGI 60 SY+GK V R K V GR YVDDI +P + + FVRS + HA I ID ++AL G+ Sbjct: 13 SYIGKTVPRPNAAKLVQGRGQYVDDITLPRMVHVAFVRSPFAHAQITGIDAAEALATKGV 72 Query: 61 VAVFTAKEINPLLKGGIRPWPTYI-DIRSFRYSERKAFPENKVKYVGEPVAIVLGQDKYS 119 + VFT ++ + PW + ++ + ++ +VGEPVA V+ + + Sbjct: 73 LRVFTGADLAEVCT----PWVAVLAHLKGLKSPPEHPIAIDRAVWVGEPVAAVVATSRAA 128 Query: 120 VRDAIDKVVVEYEPLKPVI-RMEEAEKDQVIIHEELKTNISYKIPFKAGEVDKAFSESDK 178 + V V+Y+PL V M + D +IH +L N++++ + G+VD A + + K Sbjct: 129 AEEGAALVEVDYDPLPAVTDTMTALDADTPVIHPDLGDNLAFRRLHEEGDVDAAKAAAHK 188 Query: 179 VVRVEAINERLIPNPMEPRGIVSRFEA--GTLSIWYSTQVPHYMRSEFARILGIPESKIK 236 VV R +EPR I+ + G ++ +++TQ PH M+S A+ L IPES+++ Sbjct: 189 VVTARFRTARHTGVTLEPRSILVDWNPAEGQMTAYHATQAPHMMQSVLAKHLDIPESRVR 248 Query: 237 VSMPDVGGAFGAKVHLMPEELAVVASSIILGRPVRWTATRSEEMLAS-EARHNVFTGEVA 295 V DVGG++G KVH+ P+E+A A + ++GRPV++ A R E AR + +A Sbjct: 249 VICGDVGGSYGIKVHVYPDEVATAAIAKVMGRPVKFIADRLESFTTDIHARDHEIEASIA 308 Query: 296 VKRDGTILGIKGKLLLDLGAYITV--TAGIQPLIIPMMIPGPYKIRNLDIESVAVYTNTP 353 V DG IL I +G Y T+ I+ + + GPY N + V+ N Sbjct: 309 VDADGKILAIDVNDWTGIGPYSVYPRTSAIEGNQVVNLCGGPYDFANYRARTSVVFQNKT 368 Query: 354 PITMYRGASRPEATYIIERIMSTVADELGLDDVSIREKNLVTE--LPYTNPFGLRYDSGD 411 P YR P A I E ++ A ELG+D V IR +N+ + P T+P ++++ Sbjct: 369 PTCQYRAVGHPIAVAITEGLVDMAAAELGMDPVEIRRRNMYADDAYPVTSPAKMKFEGLS 428 Query: 412 YVGLLREGVKRLGYYELKKWAEEERKKGHRVGVGLAYYLEICSFGPWEYA---------- 461 + + + + + Y L+ E RK G G+G+A ++E+ + P+ Y Sbjct: 429 HHASMDKLMAMMDYDALRADQAEARKAGKLRGLGIASFIELTNPSPFMYGIGGARISAQD 488 Query: 462 --EVRVDERGDVLVVTGTTPHGQGTETAIAQIVADALQIDISRVRVIWGDTDTVAASMGT 519 VR+D G V+ ++G T GQGTE ++Q+VA+ + + S+VRVI GDT GT Sbjct: 489 GCTVRMDPDGSVVALSGVTEQGQGTEAMLSQVVAEGVGVPPSQVRVITGDTQVTPYGGGT 548 Query: 520 YGSRSVTIGGSAAIKVAEKILDKMKRIAASTWNVDVQEVQYEKGEFKLKNDPSKKMSWDD 579 + SR IGG AA++ A+ + D + ++AA+ + G+ +++M + Sbjct: 549 WASRGAGIGGEAALQAAKALRDSILQVAAAMLQAAPDTLDIRDGQVVDAATGAERMPLAE 608 Query: 580 VASIAYRSHDP-------GLVEK---IIYENDVTFPYGVHIATVEVD-DTGVARVLEYRA 628 + I Y D LV+ I + F GV + +EVD +TGV +L++ Sbjct: 609 LGRIVYFRGDTLPKDLPRELVQTRHFITMDYPFAFTNGVQASYLEVDPETGVVTLLKHWC 668 Query: 629 YDDIGKVVNPALAEAQIHGGGVQAVGQALYEQALLNENGQLI-VTYADYYVPTAVEAPKF 687 +D G+V+NP L + QI GG VQ +G ALYE+ + +GQL+ + ADY VP A E P Sbjct: 669 VEDCGRVINPQLVDEQIRGGIVQGLGGALYEEIHYDADGQLLNGSMADYLVPMAAEMPDM 728 Query: 688 TSVFADQYHPSNYPTGSKGVGEAALIVGPAVIIRALEDA---IGTRFTKTPTTPEEILRA 744 + G+KG GEA PA ++ A+ DA +G + T+ P TPE ILRA Sbjct: 729 QIAHVET-PTGESELGAKGAGEAGTAGAPAAVMNAINDALRPLGAQVTEMPFTPERILRA 787 Query: 745 I 745 + Sbjct: 788 M 788 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: 1347 Number of extensions: 85 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: 749 Length of database: 793 Length adjustment: 41 Effective length of query: 708 Effective length of database: 752 Effective search space: 532416 Effective search space used: 532416 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