Alignments for a candidate for susB in Escherichia coli BW25113

GapMind for catabolism of small carbon sources

Alignments for a candidate for susB in Escherichia coli BW25113

Align α-glucosidase (EC 3.2.1.20) (characterized)
to candidate 18264 b4239 trehalose-6-P hydrolase (NCBI)

Query= CAZy::AAF71997.1
         (562 letters)



>FitnessBrowser__Keio:18264
          Length = 551

 Score =  649 bits (1673), Expect = 0.0
 Identities = 318/557 (57%), Positives = 401/557 (71%), Gaps = 12/557 (2%)

Query: 5   WWKKAVVYQIYPKSFNDTNGDGIGDLAGIIEKLDYLKQLGVDVIKLKPIYKSPQRDNGYD 64
           WW+  V+YQIYPKSF DT G G GDL G+I+ LDYL +LGVD I L P Y SPQ DNGYD
Sbjct: 7   WWQNGVIYQIYPKSFQDTTGSGTGDLRGVIQHLDYLHKLGVDAIWLTPFYVSPQVDNGYD 66

Query: 65  ISDYFQIHDEYGTMEDFDRLLEEVHRRGMKLIMDMVVNHTSTEHEWFKQARTSKDNPYRH 124
           +++Y  I   YGT++DFD L+ +   RG+++I+DMV NHTST+H WF++A  +K++PYR 
Sbjct: 67  VANYTAIDPTYGTLDDFDELVTQAKSRGIRIILDMVFNHTSTQHAWFREA-LNKESPYRQ 125

Query: 125 FYIWRDPKPDGSAPTNWQSKFGGSAWEYDEKTGQYYLHLFDVTQADLNWENEELRRRIYD 184
           FYIWRD +P+ + P NW+SKFGGSAW +  ++ QYYLHLF   QADLNWEN  +R  +  
Sbjct: 126 FYIWRDGEPE-TPPNNWRSKFGGSAWRWHAESEQYYLHLFAPEQADLNWENPAVRAELKK 184

Query: 185 MMHFWFQKGVDGFRLDVVNLLSKDQRFLDDDGSMPPGDGRKFYTDGPRIHEFLHEMNREV 244
           +  FW  +GVDG RLDVVNL+SKD RF +D      GDGR+FYTDGPR HEFLHEMNR+V
Sbjct: 185 VCEFWADRGVDGLRLDVVNLISKDPRFPED----LDGDGRRFYTDGPRAHEFLHEMNRDV 240

Query: 245 FSKYDVMTVGEMSSTTIDHCIKYTNPERRELNMVFNFHHLKVDYPNGEKWAVADFDFLAL 304
           F+   +MTVGEMSST+++HC +Y      EL+M FNFHHLKVDYP GEKW +A  DF+AL
Sbjct: 241 FTPRGLMTVGEMSSTSLEHCQRYAALTGSELSMTFNFHHLKVDYPGGEKWTLAKPDFVAL 300

Query: 305 KRILSEWQVEMHKGGGWNALFWCNHDQPRIVSRYGDDGKYHKESAKMLATVIHMMQGTPY 364
           K +   WQ  MH    WNALFWCNHDQPRIVSR+GD+G+Y   +AKMLA V+H MQGTPY
Sbjct: 301 KTLFRHWQQGMHNVA-WNALFWCNHDQPRIVSRFGDEGEYRVPAAKMLAMVLHGMQGTPY 359

Query: 365 IYQGEEIGMTDPKFERIDDYRDVESLNMYHILREQGKSEQEVLEILKRKSRDNSRTPMQW 424
           IYQGEEIGMT+P F RI DYRDVESLNM+  LR  G+   E+L IL  KSRDNSRTPMQW
Sbjct: 360 IYQGEEIGMTNPHFTRITDYRDVESLNMFAELRNDGRDADELLAILASKSRDNSRTPMQW 419

Query: 425 DDSENAGFTTGKPWIRVAPNYQQINVKKALEDPTSVFYHYQRLIQLRKQYDIITTGDYQL 484
            + +NAGFT G+PWI +  NYQQINV+ AL D +SVFY YQ+LI LRKQ  I+T G+YQ 
Sbjct: 420 SNGDNAGFTAGEPWIGLGDNYQQINVEAALADDSSVFYTYQKLIALRKQEAILTWGNYQD 479

Query: 485 LLEDHPDIFAYLRNGENEKLLVVNNFYGRETTFILPDDVDVNGYASEILISNYDDSPSDF 544
           LL + P ++ Y R  + + LLV+ N   RE   I P          ++++ NY+++    
Sbjct: 480 LLPNSPVLWCYRREWKGQTLLVIANL-SRE---IQPWQAGQMRGNWQLVMHNYEEASPQP 535

Query: 545 RKITLRPYESIVYYLTK 561
             + LRP+E+ V++L K
Sbjct: 536 CAMNLRPFEA-VWWLQK 551


Lambda     K      H
   0.320    0.138    0.433 

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: 1191
Number of extensions: 73
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: 562
Length of database: 551
Length adjustment: 36
Effective length of query: 526
Effective length of database: 515
Effective search space:   270890
Effective search space used:   270890
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 (21.8 bits)
S2: 53 (25.0 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

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Candidates (tab-delimited)
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Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
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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 2024 update 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