GapMind for catabolism of small carbon sources

 

Alignments for a candidate for treP in Dyella japonica UNC79MFTsu3.2

Align Alpha,alpha-trehalose phosphorylase; TPase; EC 2.4.1.64 (characterized)
to candidate N515DRAFT_1906 N515DRAFT_1906 alpha,alpha-trehalose phosphorylase

Query= SwissProt::Q8L164
         (774 letters)



>FitnessBrowser__Dyella79:N515DRAFT_1906
          Length = 1036

 Score =  538 bits (1386), Expect = e-157
 Identities = 294/751 (39%), Positives = 443/751 (58%), Gaps = 13/751 (1%)

Query: 29  RNETIFTLANGYIGMRGTFEERYSGPKNTSFNGTYINGFYEIHDIVYPEGGYGFAKIGQT 88
           ++E++F LANG +G+RG  EE  S P   SF    ++  +E   I Y E   GFA    T
Sbjct: 43  QDESLFALANGALGVRGGLEEGDS-PSQASF----LSAAWERTPIEYHERFPGFAAHTDT 97

Query: 89  MLNVADSKIIKLYVDGEEFDLLQGKILFYERVLDMKKGFVERKVKWESPTGKILEVKIKR 148
            + VAD+  I+L +      L +G+ L +ER LD+++G   R ++W SP G+ LE++ +R
Sbjct: 98  RIPVADATRIQLRLGDVPVRLAEGEWLDFERRLDLREGCYRRFLRWRSPAGETLEIEAER 157

Query: 149 IVSLNRQHLAAISFTMQPVNFTGKIRFVSAIDGNVSNINDSEDVRVGSNLKGKVLKTIDK 208
           IVSL+   L A+ + ++ V++TG +   SAI          +D R+G+ L G  L T+D 
Sbjct: 158 IVSLDEPGLLALRYRVRSVDYTGPVTLESAISTARDAAEQGDDPRIGTRLDGG-LHTVDA 216

Query: 209 SVEGLKGWIVQKTQKSNFSYACAIDNVLVADSKYEVSNSLEEDGVKVIVDLEAEKGTSYT 268
           + E    W+ Q+T  S    ACA  +            +L + GV          G + T
Sbjct: 217 AAEPDFAWVRQQTTHSGIRLACAQAHRAQDGGLDCHFANLAQHGVVHSYTGMLTPGQAVT 276

Query: 269 LNKFISYYTSK---DFDENKLVALALEEIEKAKNDGFETIEKEQEEFLNSFWKDADVIIE 325
           L K+++Y  ++   D  ++ L+A     +E A +  +  + + Q + L   W  AD+ I+
Sbjct: 277 LEKYVAYAWTEPHGDDADDALLARTRGILEAAAHLRYAGLLERQRQALAPLWDGADLAID 336

Query: 326 GDKALQQGIRFNEFHLLQSVGRDGKTNIAAKGLTGGGYEGHYFWDSDIYIMPFFLYTKPE 385
           GD A +Q +RFN FHL QS  RDG+ + AAKGLTG GYEGHYFWD++ +I+P      PE
Sbjct: 337 GDAATEQALRFNLFHLFQSSCRDGQGSAAAKGLTGEGYEGHYFWDAEAFILPVLATVAPE 396

Query: 386 IAKALVMYRYNLLDAARSRAKELGH-KGALYPWRTIDGPECSAYFPAGTAQYHINADIVY 444
           +A+ +++YR+ +LD +R  A+EL H +GALY WRTI G ECSAY+P G+AQYHINA I +
Sbjct: 397 LARGMLLYRHRILDRSRRHARELNHPRGALYAWRTISGDECSAYYPGGSAQYHINAAIAW 456

Query: 445 ALKRYVEATNDVDFLYDYGCEILFETARFWEDLGAYIPLKGNKFCINCVTGPDEYTALVD 504
           A+  YV+A+ D DFL D+G EILFETAR W D+G +   +G+ FCI+ VTGPDEY+ALVD
Sbjct: 457 AISLYVDASGDTDFLRDHGAEILFETARVWLDIGHFNARRGDAFCIHEVTGPDEYSALVD 516

Query: 505 NNAYTNYMAKMNLEYAYDIANKMKKEVPQKYQKVASKLNLKDEEIVAWKKAADNMYLPYS 564
           NN YTN MA+ +L  A   A  M    P +Y  + +++ L ++E+  W++AA+ MYLP  
Sbjct: 517 NNHYTNRMAQRHLRDAAATALWMAGAAPVEYGALCARIGLGEDEVAQWRRAAEAMYLPED 576

Query: 565 KELDIIPQDDSFLYKERI---TVDEIPEDQFPLLLHWHYLNIYRYQICKQPDVLLLMFLQ 621
             L + PQDD FL + R+      +  + + PLLL  H L IYR+Q+CKQ D LL + L 
Sbjct: 577 PRLGVFPQDDGFLDRPRLPDHLAAKPGDGKHPLLLRLHPLTIYRHQVCKQADTLLALMLA 636

Query: 622 REKFTKDELKKNYDYYEPITTHDSSLSPAIFSILANEIGYTDKAYKYFMMTARMDLDDYN 681
            +   +   ++N+DYYE +T HDS+LS + F ++A E+G   KA++YF  + R+DLDD +
Sbjct: 637 GDGVERAAKRRNFDYYESVTVHDSTLSASTFGVIAAEVGLAAKAWRYFQDSLRVDLDDSH 696

Query: 682 DNVKDGIHAASMAGTWSAVVNGFGGMRVYTNELHFEPRLPKEWNLLSFNVRYKGRKINVK 741
            N   G+H A+MAG+W  +V GFGG R    +    PRLP  W+   F +R+   ++ V+
Sbjct: 697 GNAAHGVHMAAMAGSWLGLVWGFGGFRTIDGQPALAPRLPAAWHGYRFGLRWGRAQLRVE 756

Query: 742 LTKENVVFALLEGEPIEIYYFDKKILLEKGE 772
           +    V + LL G+ +   +  ++  +  G+
Sbjct: 757 VDASGVRYTLLRGDTLAFRHDGREHTIHAGQ 787


Lambda     K      H
   0.318    0.137    0.407 

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: 1573
Number of extensions: 57
Number of successful extensions: 6
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: 774
Length of database: 1036
Length adjustment: 43
Effective length of query: 731
Effective length of database: 993
Effective search space:   725883
Effective search space used:   725883
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 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