GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Dshi_0546 in Methanospirillum stamsii Pt1

Align ABC transporter for Xylitol, ATPase component (characterized)
to candidate WP_109939172.1 DLD82_RS00420 glycine betaine/L-proline ABC transporter ATP-binding protein

Query= reanno::Dino:3607124
         (338 letters)



>NCBI__GCF_003173335.1:WP_109939172.1
          Length = 376

 Score =  155 bits (391), Expect = 2e-42
 Identities = 85/238 (35%), Positives = 133/238 (55%), Gaps = 6/238 (2%)

Query: 3   GIKIDKINKFYGTTQALFDINLDIEDGEFVVFVGPSGCGKSTLLRTLAGLEGVSSGRIEI 62
           G    +I +  G   AL +I+  ++ GE  V +G SGCGKSTLLR L  L   ++G I +
Sbjct: 8   GCTTKEIRERTGHVVALKNISFSVKKGEIFVLMGLSGCGKSTLLRCLNRLISPTAGSILL 67

Query: 63  GGRDVTTVEPADRD------LAMVFQSYALYPHMTVRENMEFGMKVNGFEPDLRKERIAE 116
            G D+ +V            + MVFQS+AL PH  +++N+ FG+++ G   + R     E
Sbjct: 68  DGEDIASVSTERMRTIRRSRMGMVFQSFALLPHKNIQDNVAFGLEIQGISAEERAGIAKE 127

Query: 117 AARVLQLEDYLDRKPGQLSGGQRQRVAIGRAIVKNPSVFLFDEPLSNLDAKLRVQMRVEL 176
              ++ L  Y +  P QLSGG +QRV + RAI  +P + L DE  S LD  +R  M+ EL
Sbjct: 128 TLDLVGLSGYENSYPDQLSGGMKQRVGLARAIASSPDILLMDEAFSALDPMIRRDMQNEL 187

Query: 177 EGLHKQLGATMIYVTHDQVEAMTMADKIVVLNRGRIEQVGSPMDLYHKPNSRFVAEFI 234
             +  +L  T+I+V+HD  EA+ +  +I ++  G I Q+G+P ++  +P + FV  F+
Sbjct: 188 LDIQDRLEKTIIFVSHDLDEALKLGTRIGLMKAGEIVQIGTPEEILTQPKNEFVERFV 245


Lambda     K      H
   0.320    0.139    0.396 

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: 279
Number of extensions: 14
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: 338
Length of database: 376
Length adjustment: 29
Effective length of query: 309
Effective length of database: 347
Effective search space:   107223
Effective search space used:   107223
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: 49 (23.5 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