GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ytfT in Tistlia consotensis USBA 355

Align Galactofuranose transporter permease protein YtfT (characterized)
to candidate WP_085121058.1 B9O00_RS01465 ABC transporter permease

Query= SwissProt::P39328
         (341 letters)



>NCBI__GCF_900177295.1:WP_085121058.1
          Length = 335

 Score =  150 bits (378), Expect = 6e-41
 Identities = 101/301 (33%), Positives = 165/301 (54%), Gaps = 12/301 (3%)

Query: 24  QLVALLLVL-LVDSLVAPHFWQVVLQDGRLFGSPIDILNRAAPVALLAIGMTLVIATGGI 82
           +++ L LV+  V SL++P+F    L +  +F    +IL+++  + +L+IGMT VI TGGI
Sbjct: 35  RMLGLALVIGAVLSLLSPYF----LTESNIF----NILDQSVVIGILSIGMTFVILTGGI 86

Query: 83  DLSVGAVMAIAGATTAAMTVAGFSLPIVLLSALGTGILAGLWNGILVAILKIQPFVATLI 142
           DLSVG+V  ++G     + +  + +P+ +L  + TG   GL +GIL+   ++  FV TL 
Sbjct: 87  DLSVGSVAGLSGIVLG-LALKDYPIPVAILLGVLTGAGVGLVSGILIGYFRLAAFVVTLG 145

Query: 143 LMVAGRGVAQLITAGQIVTFNSPDLSWFGSGSLLFLPTPVIIAVLTLILFWLLTRKTALG 202
           +M  GR +A + +    ++    DLS      +  +PT V+      +L W     T  G
Sbjct: 146 MMAIGRSLAYIFSGQTAISGFPSDLSSIVYTDVFGIPTNVLFLGFAYLLAWGYLTYTKGG 205

Query: 203 MFIEAVGINIRAAKNAGVNTRIIVMLTYVLSGLCAAIAGIIVAADIRGADANNAGLWLEL 262
             I A+G N  AA+ AG+      +L YV+SG  AA+A     A I   D    G  +EL
Sbjct: 206 RTIYAIGSNKEAARAAGLGVLFYSILPYVVSGALAAVAITFSVAQILSVDP-LTGNGMEL 264

Query: 263 DAILAVVIGGGSLMGGRFNLLLSVVGALIIQGMNTGILLSGFPP-EMNQVVKAVVVLCVL 321
           DAI AVVIGG SL GGR +++ +++G LI+  +  G+ L G  P      + +++++ +L
Sbjct: 265 DAIAAVVIGGASLYGGRGSIVGTLIGVLIMVMIRNGLNLLGVSPFWQGSAIGSIIIMALL 324

Query: 322 I 322
           +
Sbjct: 325 V 325


Lambda     K      H
   0.327    0.142    0.416 

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: 294
Number of extensions: 27
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 341
Length of database: 335
Length adjustment: 28
Effective length of query: 313
Effective length of database: 307
Effective search space:    96091
Effective search space used:    96091
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: 49 (23.5 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