Alignments for a candidate for susB in Sphingomonas koreensis DSMZ 15582

GapMind for catabolism of small carbon sources

Alignments for a candidate for susB in Sphingomonas koreensis DSMZ 15582

Align Maltose or maltodextrin glucosidase (EC 3.2.1.20) (characterized)
to candidate Ga0059261_1581 Ga0059261_1581 Glycosidases

Query= reanno::Korea:Ga0059261_1581
         (604 letters)



>FitnessBrowser__Korea:Ga0059261_1581
          Length = 604

 Score = 1224 bits (3168), Expect = 0.0
 Identities = 604/604 (100%), Positives = 604/604 (100%)

Query: 1   MRSLAFALTLLAGTVASAQTAAPAELRARAAETEVLYFLLPDRFENGDPSNDRGGLRGDR 60
           MRSLAFALTLLAGTVASAQTAAPAELRARAAETEVLYFLLPDRFENGDPSNDRGGLRGDR
Sbjct: 1   MRSLAFALTLLAGTVASAQTAAPAELRARAAETEVLYFLLPDRFENGDPSNDRGGLRGDR 60

Query: 61  LTTGFDPAHKGFFHGGDLKGLIRRLDYIQSLGASAIWLGPIYKNKPVQGGPGQETAGYHG 120
           LTTGFDPAHKGFFHGGDLKGLIRRLDYIQSLGASAIWLGPIYKNKPVQGGPGQETAGYHG
Sbjct: 61  LTTGFDPAHKGFFHGGDLKGLIRRLDYIQSLGASAIWLGPIYKNKPVQGGPGQETAGYHG 120

Query: 121 YWITDFTRVDPHFGTNDEMKAFVDAAHARGIKVYLDIITNHTADVIQYRECPKSACDYRS 180
           YWITDFTRVDPHFGTNDEMKAFVDAAHARGIKVYLDIITNHTADVIQYRECPKSACDYRS
Sbjct: 121 YWITDFTRVDPHFGTNDEMKAFVDAAHARGIKVYLDIITNHTADVIQYRECPKSACDYRS 180

Query: 181 RADYPYQRKGGVKGAAINPGFAGDGVQTPENFAKLSDPNYAYTTVVPEAERTVKVPAWLN 240
           RADYPYQRKGGVKGAAINPGFAGDGVQTPENFAKLSDPNYAYTTVVPEAERTVKVPAWLN
Sbjct: 181 RADYPYQRKGGVKGAAINPGFAGDGVQTPENFAKLSDPNYAYTTVVPEAERTVKVPAWLN 240

Query: 241 DPIHYHNRGNTTFRNESSTMGDFVGLDDLMTESPRVLQGFIDIYGAWIDQFGIDGFRIDT 300
           DPIHYHNRGNTTFRNESSTMGDFVGLDDLMTESPRVLQGFIDIYGAWIDQFGIDGFRIDT
Sbjct: 241 DPIHYHNRGNTTFRNESSTMGDFVGLDDLMTESPRVLQGFIDIYGAWIDQFGIDGFRIDT 300

Query: 301 ARHVNPEFWQGFSKAMIERAKARGIPNFHIFGEVANEGDVGDLALHTRVHQLPSVLDFGF 360
           ARHVNPEFWQGFSKAMIERAKARGIPNFHIFGEVANEGDVGDLALHTRVHQLPSVLDFGF
Sbjct: 301 ARHVNPEFWQGFSKAMIERAKARGIPNFHIFGEVANEGDVGDLALHTRVHQLPSVLDFGF 360

Query: 361 RAAVQHTVAGEKGPDMLAAMFDRDALYEGGAEAALRLPTFISNHDHGRFSTDVRKAFPKA 420
           RAAVQHTVAGEKGPDMLAAMFDRDALYEGGAEAALRLPTFISNHDHGRFSTDVRKAFPKA
Sbjct: 361 RAAVQHTVAGEKGPDMLAAMFDRDALYEGGAEAALRLPTFISNHDHGRFSTDVRKAFPKA 420

Query: 421 SDDEVLARVKLAHAMLLLLRGVPTIYSGDEQGFVSDGNDQDAREDMFPSKVAIYNDNRLL 480
           SDDEVLARVKLAHAMLLLLRGVPTIYSGDEQGFVSDGNDQDAREDMFPSKVAIYNDNRLL
Sbjct: 421 SDDEVLARVKLAHAMLLLLRGVPTIYSGDEQGFVSDGNDQDAREDMFPSKVAIYNDNRLL 480

Query: 481 GTDKTTADSNFDTGHPLYMEISKLSAIRKATPALSRGRQVTRAYDEKPGLFAVSRFDPAS 540
           GTDKTTADSNFDTGHPLYMEISKLSAIRKATPALSRGRQVTRAYDEKPGLFAVSRFDPAS
Sbjct: 481 GTDKTTADSNFDTGHPLYMEISKLSAIRKATPALSRGRQVTRAYDEKPGLFAVSRFDPAS 540

Query: 541 GAEVLVAFNTSAAPITRQVEVGVSSTAFAPLVGQCAASASAPGSVTVTLPAFGYVACVAA 600
           GAEVLVAFNTSAAPITRQVEVGVSSTAFAPLVGQCAASASAPGSVTVTLPAFGYVACVAA
Sbjct: 541 GAEVLVAFNTSAAPITRQVEVGVSSTAFAPLVGQCAASASAPGSVTVTLPAFGYVACVAA 600

Query: 601 GGAK 604
           GGAK
Sbjct: 601 GGAK 604


Lambda     K      H
   0.319    0.136    0.411 

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: 1476
Number of extensions: 45
Number of successful extensions: 1
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: 604
Length of database: 604
Length adjustment: 37
Effective length of query: 567
Effective length of database: 567
Effective search space:   321489
Effective search space used:   321489
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 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