GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aldox-large in Dinoroseobacter shibae DFL-12

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.

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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