GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__Dyella79:N515DRAFT_1906 N515DRAFT_1906
           alpha,alpha-trehalose phosphorylase
          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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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