GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SM_b21106 in Paucidesulfovibrio gracilis DSM 16080

Align ABC transporter for L-Fucose, ATPase component (characterized)
to candidate WP_078716157.1 B5D49_RS02895 glycine betaine/L-proline ABC transporter ATP-binding protein

Query= reanno::Smeli:SM_b21106
         (365 letters)



>NCBI__GCF_900167125.1:WP_078716157.1
          Length = 396

 Score =  158 bits (399), Expect = 3e-43
 Identities = 84/222 (37%), Positives = 130/222 (58%), Gaps = 6/222 (2%)

Query: 19  VHGIDLEVKDREFIALVGPSGCGKSTTLRMIAGLEEVSGGAIEIGGRKVNDLPP------ 72
           V+    +V++ E + ++G SG GKST +R I  L E + G + I G++V  L        
Sbjct: 43  VNDASFQVEEGEIVVVMGLSGSGKSTLVRCINRLIEPTAGTVRIDGQEVTKLDDKGLRDL 102

Query: 73  RARNISMVFQSYALYPHMTVAENMGFSLKIAGRPAEEIKTRVAEAAAILDLAHLLERRPS 132
           R   ++MVFQ++AL+PH TVA+N  + L+I G      + +  EA  ++ L    +  P 
Sbjct: 103 RLSKLAMVFQNFALFPHRTVADNTAYGLEIKGVDPATRRQKAMEALDLVGLNGWEDSMPG 162

Query: 133 QLSGGQRQRVAMGRAIVRQPDVFLFDEPLSNLDAKLRTQVRTEIKKLHARMQATMIYVTH 192
           QLSGG +QRV + RA+    D+ L DE  S LD  +R+ ++ E+  L  +M  T+++++H
Sbjct: 163 QLSGGMQQRVGLARALALDADILLMDEAFSALDPLIRSDMQDELINLQEKMHKTILFISH 222

Query: 193 DQVEAMTLSDRIVIMRDGHIEQVGTPEDVFRRPATKFVAGFI 234
           D  EA+ L DRIV+M+DG I QVGT ED+   PA  +V  F+
Sbjct: 223 DLDEAIKLGDRIVLMKDGAIVQVGTAEDILTHPANDYVERFV 264


Lambda     K      H
   0.320    0.137    0.397 

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: 295
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: 365
Length of database: 396
Length adjustment: 30
Effective length of query: 335
Effective length of database: 366
Effective search space:   122610
Effective search space used:   122610
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 50 (23.9 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