GapMind for catabolism of small carbon sources

 

Alignments for a candidate for BPHYT_RS24005 in Jannaschia aquimarina GSW-M26

Align Polar amino acid ABC transporter, inner membrane subunit; Flags: Precursor (characterized, see rationale)
to candidate WP_043917275.1 jaqu_RS02045 ABC transporter permease subunit

Query= uniprot:B2TBJ7
         (240 letters)



>NCBI__GCF_000877395.1:WP_043917275.1
          Length = 237

 Score =  172 bits (435), Expect = 7e-48
 Identities = 90/229 (39%), Positives = 138/229 (60%), Gaps = 1/229 (0%)

Query: 3   LIQMLGFGPEGWGGVLLLAALMTVALTLAALAVGAVFGALVAAAKLSRFRTLRVIGDIYT 62
           + + L F   GWGG LL   + T+ + L A A+G   G L A  K+     LR   ++YT
Sbjct: 4   VFEYLAFSAPGWGGNLLRGLVSTLQIALGAYALGMSIGILGALGKIHGGPILRGALEVYT 63

Query: 63  TVFRGVPELLVIYLFYFGGSTLVTSVGQLFGAEGFVGVPPFVVGALAVGMISGAYQAEVY 122
           T+ R VPEL++I L ++ G   +  +    G E  + +    VG   +G + GAY  EV+
Sbjct: 64  TLIRAVPELVLILLLFYAGQDAINVILTSLGFERVI-LDGLWVGIYVIGFVQGAYSTEVF 122

Query: 123 RSAVLAVSRGELEAARSIGMPTLTMARRILIPQVLRFALPGIGNVWQLSLKDSALISVTG 182
           R A  AV+ G++EAAR+IGM  L +  R++IP +L FALPG+ N+W ++ KD+AL++V G
Sbjct: 123 RGAFGAVAPGQIEAARAIGMSRLKVQTRVVIPLMLPFALPGLANLWLITTKDTALLAVVG 182

Query: 183 LAELLRTSQVAAGSTHQYFTFFVVGGALYLIMTSISNRVFNRAEAHVGR 231
           ++EL   ++ AAG+T  YF F+V  G LYL++T +SN++F   E  + R
Sbjct: 183 VSELALETRQAAGATRAYFLFYVAAGCLYLLVTLVSNQIFAWLERRLRR 231


Lambda     K      H
   0.327    0.141    0.403 

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: 134
Number of extensions: 4
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: 240
Length of database: 237
Length adjustment: 23
Effective length of query: 217
Effective length of database: 214
Effective search space:    46438
Effective search space used:    46438
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 (21.7 bits)
S2: 46 (22.3 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