GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SMc02869 in Collinsella tanakaei YIT 12063

Align N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized)
to candidate WP_009140161.1 HMPREF9452_RS00665 amino acid ABC transporter ATP-binding protein

Query= reanno::Smeli:SMc02869
         (352 letters)



>NCBI__GCF_000225705.1:WP_009140161.1
          Length = 260

 Score =  150 bits (380), Expect = 3e-41
 Identities = 92/254 (36%), Positives = 145/254 (57%), Gaps = 11/254 (4%)

Query: 8   SSFNPRGRHVGSL-----QLKTIRKAFGSHEVLKGIDLDVKDGEFVIFVGPSGCGKSTLL 62
           +S NP G    ++     Q+  + KA+G + VL+GIDLDV  GE V+ +GPSG GKST+L
Sbjct: 5   TSNNPNGGAADAIEEPVVQIHGLHKAYGDNVVLRGIDLDVHRGEVVVVLGPSGSGKSTML 64

Query: 63  RTIAGLEDATSGSVQIDGVEVG----HVAPAKRGIAMVFQSYALYPHLTVKDNMGLGLKQ 118
           R +  LE  T+GS+ ++GV++      +   +  + MVFQ + L+PHL+ K N+ +  ++
Sbjct: 65  RCVNLLETPTNGSIVVEGVDITKKGVEINKVRSTLGMVFQQFNLFPHLSAKRNVMIAQQK 124

Query: 119 AGVPKAEIEEKVAK-AAGMLSLEPYLARRPAELSGGQRQRVAIGRAIVREPKLFLFDEPL 177
                 E  E++A+     + L   +   P++LSGGQ+QRVAI RA+   P + LFDE  
Sbjct: 125 VLKRSKEEAERIAEMELAKVGLADRVDFMPSQLSGGQQQRVAIARALAMNPHVMLFDEAT 184

Query: 178 SNLDAALRVNTRLEIARLHRSLKATMIYVTHDQVEAMTLADKIVVLNAGRIEQVGSPMEL 237
           S LD  L V   L + R       TMI VTH+   A  +AD+++ ++ G I + G+P E+
Sbjct: 185 SALDPEL-VRDVLGVMRDLARGGMTMIVVTHEMGFARDVADRVIFMDGGVIVEQGTPEEV 243

Query: 238 YNRPANLFVAGFIG 251
           ++ P +     F+G
Sbjct: 244 FDHPKSERTKDFLG 257


Lambda     K      H
   0.320    0.137    0.393 

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: 234
Number of extensions: 10
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: 352
Length of database: 260
Length adjustment: 27
Effective length of query: 325
Effective length of database: 233
Effective search space:    75725
Effective search space used:    75725
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: 48 (23.1 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