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

GapMind for catabolism of small carbon sources

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

Align α,α-trehalase (MSMEG_4535;MSMEG4528) (EC 3.2.1.28) (characterized)
to candidate N515DRAFT_1888 N515DRAFT_1888 Glucoamylase (glucan-1,4-alpha-glucosidase), GH15 family

Query= CAZy::ABK72415.1
         (668 letters)



>FitnessBrowser__Dyella79:N515DRAFT_1888
          Length = 620

 Score =  252 bits (643), Expect = 4e-71
 Identities = 198/624 (31%), Positives = 289/624 (46%), Gaps = 55/624 (8%)

Query: 46  GFLSDCETTCLISSAGSVEWLCVPRPDSPSVFGAILD--RGAGHFRLGPYGVSVPAARRY 103
           G + +     LI     + W C+PR DS + F A+L   R  G + +    V   A + Y
Sbjct: 35  GVIGNGSIAALIDGMARIVWCCLPRFDSDASFCALLSPQREGGDWIIELEHVE-RAEQEY 93

Query: 104 LPGSLILETT-WQTHTGWLIVRDALVMGPWHDIDTRSRTHRRTPMDWDAEHILLRTVRCV 162
           LP + +L T  +  H   + + D     P H    RSR     P+      +L R +R +
Sbjct: 94  LPNTAVLVTRLYDRHDNAIEITD---FAPRH----RSRGRFYHPV------MLARRIRPI 140

Query: 163 SGTVELVMSCEPAFDYHRVSATWEYSGPAYGEAIARASRNPDSHPTLRLTTNLRIGIEGR 222
            G   + +   P  DY    A    SG  +   +        S    RLTT++ + +  R
Sbjct: 141 QGKPRIRILLRPLCDYG-ARAPETTSGSNHLRFLL-------SDVIQRLTTDVAVPLIER 192

Query: 223 EARARTRLTEGDNVFVALSWSKH----PAPQTYEEAADKMWKTSEA----WRQWINVGDF 274
                        +F  L    H    P        AD +  + E     WR W+     
Sbjct: 193 ------------GLFFHLDRPAHLVFGPDETLVTSPADFIHSSLEYTIAYWRDWVRYLSI 240

Query: 275 PDHPWRAYLQRSALTLKGLTYSPTGALLAAPTTSLPETPQGERNWDYRYSWIRDSTFALW 334
           P + W+  + R+A+TLK   Y  TGA++AA TTS+PE P   RNWDYRY W+RD+ F + 
Sbjct: 241 P-YEWQEPVIRAAITLKLCQYEATGAIIAALTTSIPEAPGTRRNWDYRYCWLRDAAFVVR 299

Query: 335 GLYTLGLDREADDFFSFIADVSGANNGERHPLQVMYGVGGERSLVEEELHHLSGYDNSRP 394
            L  LG  R  +++  ++ ++  A     H +  ++G+  ER L E E   L GY    P
Sbjct: 300 ALNRLGATRSMEEYIRYVFNIFSAEGD--HEVGPVFGITFERELPEREAAGLDGYRGMGP 357

Query: 395 VRIGNGAYNQRQHDIWGT-MLDSVYLHAKSR-EQIPDA-LWPVLKNQVEEAIKHWKEPDR 451
           VRIGN A+ QRQ+D++G+ +L S  L    R E   DA  +  L++    A++  +EPD 
Sbjct: 358 VRIGNDAWRQRQNDVYGSVVLASAQLFFDQRLENRGDARTFQRLESMGRMALRMAEEPDA 417

Query: 452 GIWEVRGEPQHFTSSKIMCWVALDRGSKLAELQGEKSYAQQWRAIAEEIKADVLARGVDK 511
           G+WE RG     T S  MCW A DR + +A   G K  A+ W   A  +   +  R  ++
Sbjct: 418 GLWEFRGRAAVHTYSAAMCWAACDRLAHIATELGLKDRARYWHDEAVALHERISKRIWNE 477

Query: 512 R-GVLTQRYGDDALDASLLLAVLTRFLPADDPRIRATVLAIADELTEDGLVLRYRVEETD 570
           R G     Y  + LDASLLL     F+   DPR  ATV AI   L     + RY      
Sbjct: 478 RLGHFVDAYDGEHLDASLLLLADIGFVRGRDPRFIATVDAIGKALGRGDYLFRY---IAP 534

Query: 571 DGLAGEEGTFTICSFWLVSALVEIGEISRAKHLCERLLSFASPLHLYAEEIEPRTGRHLG 630
           D     E +F IC+FW + AL   G   RA+ + E +L+  +PL L +E+I P TG H G
Sbjct: 535 DDFGAPETSFNICTFWYIEALAATGRKRRARLMFEHMLAQRNPLGLLSEDIAPGTGEHWG 594

Query: 631 NFPQAFTHLALINAVVHVIRAEEE 654
           NFPQ ++ + LI   + + R  E+
Sbjct: 595 NFPQTYSLVGLIQTAMRLSRRWED 618


Lambda     K      H
   0.319    0.135    0.426 

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: 1153
Number of extensions: 57
Number of successful extensions: 6
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: 668
Length of database: 620
Length adjustment: 38
Effective length of query: 630
Effective length of database: 582
Effective search space:   366660
Effective search space used:   366660
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: 54 (25.4 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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Protein sequences (fasta format)
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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources