GapMind for catabolism of small carbon sources

 

Alignments for a candidate for TM0027 in Rhizorhabdus wittichii RW1

Align TM0027, component of β-glucoside porter (Conners et al., 2005). Binds cellobiose, laminaribiose (Nanavati et al. 2006). Regulated by cellobiose-responsive repressor BglR (characterized)
to candidate WP_012048833.1 SWIT_RS13320 amino acid ABC transporter ATP-binding protein

Query= TCDB::Q9WXN4
         (268 letters)



>NCBI__GCF_000016765.1:WP_012048833.1
          Length = 241

 Score =  112 bits (281), Expect = 6e-30
 Identities = 82/234 (35%), Positives = 124/234 (52%), Gaps = 10/234 (4%)

Query: 25  AVKNVSFEVKEKEIVSLVGESGSGKTTTAKMILRLLPPTSGEIYFEGKDIWKDIKDRESL 84
           A++NVS +V   E + + G SGSGK+T  + I  L     G I   G+D  +   DR  L
Sbjct: 16  ALRNVSLDVARGERIVICGPSGSGKSTLIRCINGLETHDEGVIRI-GEDEVRP--DRRVL 72

Query: 85  VEFRRKVHAVFQDPFASYNPFYPVERTLWQAISLLENKPSNKKEALELIKESLFRVGIDP 144
              R +V  VFQD    +N F  +      A++ ++ +   +  A  L +E L RV I  
Sbjct: 73  QRIRARVGMVFQD----FNLFPHLTILENCALAPMKVRGLARDAAEALARELLERVRI-- 126

Query: 145 KDVLGKYPHQISGGQKQRIMIARCWILRPLLIVADEPTSMIDASSRGGIIKLLEELREEQ 204
            D   KYP Q+SGGQ+QR  IAR   ++P +I+ DEPTS +DA     ++ +++ L  E 
Sbjct: 127 ADQADKYPAQLSGGQQQRTAIARALAMQPEIILFDEPTSALDAEMVKEVLDIMKALATE- 185

Query: 205 GTSIIFITHDLGLAYYVSDNIFVMKNGEIVERGHPDKVVLEPTHEYTKLLVGSI 258
           G +++ +TH++G A  V+D I  M  G+IVE G P      P HE T+  +  +
Sbjct: 186 GITMLCVTHEMGFAREVADRIIFMDAGQIVETGSPRDFFTAPCHERTRAFLSRL 239


Lambda     K      H
   0.319    0.139    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: 150
Number of extensions: 8
Number of successful extensions: 3
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: 268
Length of database: 241
Length adjustment: 24
Effective length of query: 244
Effective length of database: 217
Effective search space:    52948
Effective search space used:    52948
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 (21.7 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