GapMind for catabolism of small carbon sources

 

Aligments for a candidate for malE_Aa in Escherichia coli BW25113

Align Maltodextrin-binding protein (characterized, see rationale)
to candidate 18062 b4034 maltose ABC transporter periplasmic protein (NCBI)

Query= uniprot:Q9RHZ6
         (427 letters)



>lcl|FitnessBrowser__Keio:18062 b4034 maltose ABC transporter
           periplasmic protein (NCBI)
          Length = 396

 Score =  176 bits (446), Expect = 1e-48
 Identities = 121/383 (31%), Positives = 195/383 (50%), Gaps = 18/383 (4%)

Query: 48  ASALPKGQTITVWSWQTGPE-LQDVKQIAAQWAKAHGDKVIVVDQSSNPKGFQFYATAAR 106
           ASAL K +   +  W  G +    + ++  ++ K  G KV V       + F      A 
Sbjct: 22  ASALAKIEEGKLVIWINGDKGYNGLAEVGKKFEKDTGIKVTVEHPDKLEEKFP---QVAA 78

Query: 107 TGKGPDVVFGMPHDNNGVFAEEGLMAPV-PSGVLNTGLYAPNTIDAIKVNGTMYSVPVSV 165
           TG GPD++F   HD  G +A+ GL+A + P       LY P T DA++ NG + + P++V
Sbjct: 79  TGDGPDIIF-WAHDRFGGYAQSGLLAEITPDKAFQDKLY-PFTWDAVRYNGKLIAYPIAV 136

Query: 166 QVAAIYYNKKLVPQPPQTWAEFV---KDANAHG---FMYDQANLYFDYAIIGGYGGYVFK 219
           +  ++ YNK L+P PP+TW E     K+  A G    M++    YF + +I   GGY FK
Sbjct: 137 EALSLIYNKDLLPNPPKTWEEIPALDKELKAKGKSALMFNLQEPYFTWPLIAADGGYAFK 196

Query: 220 DNNGTLDPNNIGLDTPGAVQAYTLMRDMVSKYHWMTPSTNGSIAKAEFLAGKIGMYVSGP 279
             NG  D  ++G+D  GA    T + D++   H M   T+ SIA+A F  G+  M ++GP
Sbjct: 197 YENGKYDIKDVGVDNAGAKAGLTFLVDLIKNKH-MNADTDYSIAEAAFNKGETAMTINGP 255

Query: 280 WDTADIEKAKIDFGVTPWPTLPNGKHATPFLGVITAFVNKES-KTQAADWSLVQALTSAQ 338
           W  ++I+ +K+++GVT  PT   G+ + PF+GV++A +N  S   + A   L   L + +
Sbjct: 256 WAWSNIDTSKVNYGVTVLPTF-KGQPSKPFVGVLSAGINAASPNKELAKEFLENYLLTDE 314

Query: 339 AQQMYFRDSQQIPALLSVQRSSAVQSSPTFKAFVEQLRYAVPMPNIPQMQAVWQAM-SIL 397
             +   +D + + A+        +   P   A +E  +    MPNIPQM A W A+ + +
Sbjct: 315 GLEAVNKD-KPLGAVALKSYEEELAKDPRIAATMENAQKGEIMPNIPQMSAFWYAVRTAV 373

Query: 398 QNIIAGKVSPEQGAKDFVQNIQK 420
            N  +G+ + ++  KD    I K
Sbjct: 374 INAASGRQTVDEALKDAQTRITK 396


Lambda     K      H
   0.315    0.130    0.392 

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: 446
Number of extensions: 38
Number of successful extensions: 7
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: 427
Length of database: 396
Length adjustment: 31
Effective length of query: 396
Effective length of database: 365
Effective search space:   144540
Effective search space used:   144540
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 50 (23.9 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