GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Keio:18062
          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:

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