GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ac3H11_2555 in Desulfoscipio geothermicus DSM 3669

Align ABC transporter for L-Histidine, periplasmic substrate-binding component 1 (characterized)
to candidate WP_092482462.1 BM299_RS05460 amino acid ABC transporter substrate-binding protein

Query= reanno::acidovorax_3H11:Ac3H11_2555
         (249 letters)



>NCBI__GCF_900115975.1:WP_092482462.1
          Length = 285

 Score =  128 bits (322), Expect = 1e-34
 Identities = 79/241 (32%), Positives = 129/241 (53%), Gaps = 8/241 (3%)

Query: 11  SLAAAAFCTTGAQAQDN-VLRVGTDATFPPMEFV-ENGKRTGFDIELVEAIAKTMGKQVE 68
           +++A A  TT    Q+  V+ +G D TF PM F  ENG+  GFDI++ +   K +G ++E
Sbjct: 35  AVSADAEKTTWELIQEKGVMTIGLDDTFRPMGFRDENGQLVGFDIDMGKEFEKRLGVKME 94

Query: 69  WVDIDFKGLIPGLISKRFDMAVSAIYITDERKKVVDFTDSYYAGGLVVMVKADNKAINKL 128
           W+  D+ G+   L SK+FD+ ++ + IT+ERKKV+DF+  Y    + + V+ DN  I   
Sbjct: 95  WIPTDWSGVTGALNSKKFDVVINGMSITEERKKVIDFSIPYVNASIGMAVQKDNNDIKTR 154

Query: 129 ADLDGKKVSVQVGT---KSVSYLTEK--FPKVQRVEVEKNQEMFNLVDIGRADAAVTGKP 183
            DL GK V+ Q G+   ++   L E     +    +  +  E F  +  GR D  V    
Sbjct: 155 DDLKGKTVATQAGSSGYEACKKLVEDGIIDETNLKQYNQYPEAFQDLAFGRVDVVVVDVT 214

Query: 184 AAFQYVRTRPG-LRVLDEQLTTEEYGMALRKDTPELTKAVNGAITKLKADGTYAAIVKKW 242
            A  +V  RP   +V++E L  + Y + LRK+  +L + ++  + ++  DGT   I K+W
Sbjct: 215 TAQDFVNKRPDTYKVVEEPLVEDFYAIGLRKEDKDLKEVLDKTLREMMEDGTLVEISKRW 274

Query: 243 F 243
           F
Sbjct: 275 F 275


Lambda     K      H
   0.317    0.133    0.369 

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: 198
Number of extensions: 12
Number of successful extensions: 4
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: 249
Length of database: 285
Length adjustment: 25
Effective length of query: 224
Effective length of database: 260
Effective search space:    58240
Effective search space used:    58240
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 (21.7 bits)
S2: 47 (22.7 bits)

This GapMind analysis is from Apr 09 2024. 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