GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aldox-large in Pseudomonas fluorescens FW300-N2C3

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.

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About GapMind

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:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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