Align glycolaldehyde oxidoreductase large subunit (characterized)
to candidate AO356_26665 AO356_26665 carbon monoxide dehydrogenase
Query= metacyc::MONOMER-18071 (749 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_26665 Length = 999 Score = 306 bits (783), Expect = 4e-87 Identities = 236/797 (29%), Positives = 376/797 (47%), Gaps = 70/797 (8%) Query: 3 YVGKPVKRIYDDKFVTGRSTYVDDIRIP--ALYAGFVRSTYPHAIIKRIDVSDALKVNGI 60 ++G R+ D + G Y DD IP L+A +RS + HA I +D S AL + G+ Sbjct: 14 HIGARQTRVEDAALLRGLGCYADDAAIPPGTLHAAIIRSPHAHARITSVDFSSALLMKGV 73 Query: 61 VAVFTAKEINPLLKGGIRPWPTYIDIRSFRYSERKAFPENKVKYVGEPVAIVLGQDKYSV 120 V +++ + W + + E +KV+YVGEPVA+V+ + +Y Sbjct: 74 HGVLVGEDV--------KRWALPFPVGVRQPMEHWCVAVDKVRYVGEPVAVVIAESRYLA 125 Query: 121 RDAIDKVVVEYEPLKPVIRMEEAEKDQV-IIHEELKTNISYKIPFKAGEVDKAFSESDKV 179 DAI+ V VEYEPL P+I E A +Q I+HE + +N+ + F+ GE ++AF ++ Sbjct: 126 EDAIEGVRVEYEPLPPIIDPERATAEQAPILHEAVGSNVVNERRFRYGEPEQAFEQAPHK 185 Query: 180 VRVEAINERLIPNPMEPRGIVSRFE--AGTLSIWYSTQVPHYMRSEFARILGIPESKIKV 237 V ++ R P+E +++++E G + + Q P+ + + AR L +P +++++ Sbjct: 186 VSLKVKFPRSSCTPIECYVVLAQYERATGIYDVLANFQGPYALHTVMARALNVPGNRLRL 245 Query: 238 SMP-DVGGAFGAKVHLMPEELAVVASSIILGRPVRWTATRSEEML-ASEARHNVFTGEVA 295 P D GG+FG K + P + + +S +G PV+W R E + AS A + V E A Sbjct: 246 RTPKDSGGSFGIKQGVFPYVVMMGLASRKVGAPVKWVEDRLEHLQGASSATNRVTEIEAA 305 Query: 296 VKRDGTILGIKGKLLLDLGAYITVTAGIQPLIIPMMIPGPYKIRNLDIESVAVYTNTPPI 355 V+ DG I ++ + D GAY+ + + G Y IRNL + + V TN P Sbjct: 306 VEADGRITALRYDQIDDCGAYLRAPEPATFYRMHGNLTGAYAIRNLQVRNRVVLTNKTPS 365 Query: 356 TMYRGASRPEATYIIERIMSTVADELGLDDVSIREKNLV--TELPYTNPFGLRYDSGDYV 413 + RG P+ + +ER+M +A +L LD + + +NLV PY G DSG+Y Sbjct: 366 GLNRGFGGPQVYFALERLMQHIAVQLKLDPLDVIRRNLVPADAFPYRAAAGALLDSGNYQ 425 Query: 414 GLLREGVKRLGYYELKKWAEEERKKGHRVGVGLAYYLE--ICSFG-------PWE----- 459 + G EL K ++ R +G G+G A +E I + G P E Sbjct: 426 AGIALAAADGGLDELLKRRDQARAEGRIYGIGYAAVIEPSISNMGYITTAMTPEERRKAG 485 Query: 460 -------YAEVRVDERGDVLVVTGTTPHGQGTETAIAQIVADALQIDISRVRV-IWGDT- 510 A + V GDV V + P GQG +T +AQ+VA+ L + + + V + DT Sbjct: 486 PKNGAVATATINVGPLGDVSVHVSSAPQGQGHQTTVAQVVAEVLGVALESIVVNVELDTQ 545 Query: 511 -DTVAASMGTYGSRSVTIGGSAAIKVAEKILDKMKRIAASTWNVDVQEVQYEKGEFKLKN 569 D + + G Y SR A K A KI D++ IAA +++++ G+ + N Sbjct: 546 KDAWSIASGNYSSRFAGAVAGAVYKAALKIRDRLAAIAAEQLQASPEDIRFAGGKIFVVN 605 Query: 570 D----PSKKMS----WDDVASIAYRSHDPGLVEKIIY--------------ENDVTFPYG 607 P +++ W + GL E + + + + + Sbjct: 606 GGAVAPFHRIAGATHWS--PGLLPEGESGGLRETAFWSPPQLVAPDDQDQVNSSLCYGFV 663 Query: 608 VHIATVEVDD-TGVARVLEYRAYDDIGKVVNPALAEAQIHGGGVQAVGQALYEQALLNEN 666 I +E+D TG + Y D G+++NPAL + QI GG Q +G AL E+ E+ Sbjct: 664 FDICGLEIDRMTGEIHIDRYVTCHDAGRLLNPALVDGQIRGGFTQGLGAALMEEFAYGED 723 Query: 667 GQLIV-TYADYYVPTAVEAPKFTSVFADQYHPSNY-PTGSKGVGEAALIVGPAVIIRALE 724 G + T+ADY VPTA EA V PS + P G+KGVGE + P I A+ Sbjct: 724 GSFLSGTFADYLVPTAPEA--IEPVILHMETPSPFTPLGAKGVGEGNNMSTPVCIANAVA 781 Query: 725 DAIGTRFTKTPTTPEEI 741 DA+G + P TP ++ Sbjct: 782 DALGRSDIRLPLTPSKV 798 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: 1704 Number of extensions: 100 Number of successful extensions: 12 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 749 Length of database: 999 Length adjustment: 42 Effective length of query: 707 Effective length of database: 957 Effective search space: 676599 Effective search space used: 676599 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: 56 (26.2 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