GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malG_Aa in Caldicellulosiruptor kronotskyensis 2002

Align Binding-protein-dependent transport systems inner membrane component (characterized, see rationale)
to candidate WP_013429352.1 CALKRO_RS01420 sugar ABC transporter permease

Query= uniprot:C8WUQ9
         (301 letters)



>NCBI__GCF_000166775.1:WP_013429352.1
          Length = 289

 Score =  263 bits (672), Expect = 4e-75
 Identities = 126/286 (44%), Positives = 188/286 (65%), Gaps = 8/286 (2%)

Query: 24  RRSMQPGEQVALWVSRIVIWCVIVMVLLPMWFVVIASFNPSNSYISFSLFPSNASLANYK 83
           R  M   + + LW+SR++IW  I++ LLP WF+++AS +   ++   S FP   +  NY 
Sbjct: 4   REYMTKQDAIVLWISRVIIWVAIILSLLPTWFIIVASLSKGGAFFQSSFFPKEITFENYI 63

Query: 84  ALFQGGQ--------FWTWVRNSLVVGVVVAMAQSFITAMSAFAFSKLRFYGRKYGLMTL 135
            LF+           F  WV+NSL+V   VA  Q F+TA +A+AFS++ F GRK GL TL
Sbjct: 64  ELFRRKSSPSQTLPDFVMWVKNSLIVCFGVAFLQIFMTAPAAYAFSRINFVGRKNGLKTL 123

Query: 136 LLLQMFPNILAIAAFYTALAKLNMIDMLGSYILVMLGTSAFNIWLLKGYMDSVPKELDEA 195
           L+LQMFP  +A+ A Y  LAK N++D L + ILV+ G SAFNIWLLKG MD +P E+DEA
Sbjct: 124 LILQMFPTFMAMPAIYGLLAKFNLLDNLFALILVLAGGSAFNIWLLKGNMDQIPYEIDEA 183

Query: 196 AVIDGATTWQRFIHVTLPLSTPMMVVIFFLTLVGIFSEYMFAGTILQSPWNYTLGVGMYN 255
           A+IDGA  +  F  + LPL+ PM+ V+F  +  G+F+E++ +  +LQSP N T+ +G+ N
Sbjct: 184 AIIDGAGHFLIFRKIILPLTAPMLAVMFIWSFNGVFNEFLLSSLVLQSPENATVPIGLRN 243

Query: 256 LISGQFAKNWGEFAAAALLSAVPLAIVFAVAQRYLTKGLVAGSVKG 301
            I+ QF+ NW  F+AA++L+++P+ I++   Q+ +  GL AG++KG
Sbjct: 244 FINNQFSANWPMFSAASILASLPIVIIYMALQKQIQSGLAAGAIKG 289


Lambda     K      H
   0.328    0.136    0.417 

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: 286
Number of extensions: 15
Number of successful extensions: 2
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: 301
Length of database: 289
Length adjustment: 26
Effective length of query: 275
Effective length of database: 263
Effective search space:    72325
Effective search space used:    72325
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 48 (23.1 bits)

This GapMind analysis is from Sep 24 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