GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aglF in Jannaschia aquimarina GSW-M26

Align Inner membrane ABC transporter permease protein (characterized, see rationale)
to candidate WP_043920091.1 jaqu_RS16540 sugar ABC transporter permease

Query= uniprot:A8LLL5
         (334 letters)



>NCBI__GCF_000877395.1:WP_043920091.1
          Length = 319

 Score =  122 bits (307), Expect = 9e-33
 Identities = 91/277 (32%), Positives = 135/277 (48%), Gaps = 21/277 (7%)

Query: 54  WIFLFPALFVLLLYLGYPVVETLRLSL-------LERVPGGGYQWVGLDNYAQMASEPKF 106
           WIF+ P +F+LL    +P++ T+RLS        L R P    +WVGL NY ++ ++   
Sbjct: 35  WIFVAPTIFLLLAVNIFPLIWTIRLSFTNYRANRLNREP----EWVGLRNYERILTDSDT 90

Query: 107 WEAMRNNMFWLIVVPALSTAFGLLAAQLTDR-IKWGNVAKSIIFMPMAISFVGASVIWKL 165
           W +M+    +LI   AL    G   A L +R  K      +II +PM +S       W  
Sbjct: 91  WASMQATAHFLIWTIALQVLIGFALAWLINRQFKGSAFWTTIIVLPMMLSPAVVGNFWSF 150

Query: 166 VYDGRPIEQEQIGILNAIIVGLGG-DPVTFLTIPFWN--NFFLMIVLVWVQTGFAMVILS 222
           +Y      Q QI + N +I  L G DP +F  +   N   + ++IV  W+ T F M+I  
Sbjct: 151 LY------QPQIRLFNYVIAFLSGQDPSSFDILGSVNLAPWAIVIVDTWMWTPFVMLICL 204

Query: 223 AALRGIPEETIEAAIIDGASPLQIFFKIKVPQIMPTVVVVWTTITLVVLKVFDIVFAMTN 282
           A LR IP+   EAA +D ASP++ FF I VP ++P +++      +   K+FD+V  +T 
Sbjct: 205 AGLRSIPDYLYEAAAVDRASPIRQFFTITVPMVLPFLMLAVLFRGIENFKMFDLVVQLTG 264

Query: 283 GQWETQVLANYMFDKLFRANDWGVGSASAMVIMLLVT 319
           G          +  K      W  G ASA  I+L VT
Sbjct: 265 GGPGNITTLTSIDLKREAFEKWRTGYASAYAIILFVT 301


Lambda     K      H
   0.329    0.143    0.455 

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: 311
Number of extensions: 21
Number of successful extensions: 3
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: 334
Length of database: 319
Length adjustment: 28
Effective length of query: 306
Effective length of database: 291
Effective search space:    89046
Effective search space used:    89046
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