GapMind for catabolism of small carbon sources

 

Alignments for a candidate for TM0028 in Methanobacterium lacus AL-21

Align TM0028, 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_013645374.1 METBO_RS08905 ABC transporter ATP-binding protein

Query= TCDB::Q9WXN5
         (330 letters)



>NCBI__GCF_000191585.1:WP_013645374.1
          Length = 223

 Score = 93.2 bits (230), Expect = 5e-24
 Identities = 70/233 (30%), Positives = 128/233 (54%), Gaps = 18/233 (7%)

Query: 5   LLKAENVRAYYKLEKVSVKAVDGLSFEILEDEVIGVVGESGCGKTTLSNVIFMNMVKPLT 64
           ++K +N++  Y  E  S+ A++ +  EI   E + ++G SG GK+TL     +NM+  L 
Sbjct: 6   IIKIKNLKKEY--EDGSIIALNNVDLEIERGESVSIIGPSGSGKSTL-----LNMIGGLD 58

Query: 65  LVDGKIFLRVNGEFVELSSMTRDEVKRKFWGKEITIIPQAAMNALMPTIRMEKYVRHLAE 124
             +           ++ S ++       F   EI  + Q  ++ L+P + + + V+    
Sbjct: 59  KANEGQISVAGVNLMDNSDLSN------FRSNEIGFVFQ--LHNLIPNLTVLENVQIPLL 110

Query: 125 SHGIDEEELLDKARRRFEEVGLDPLWIKRYPFELSGGMRQRAVIAIATILNPSLLIADEP 184
              ID++++ ++A +  + V L+   + + P +LSGG RQR  IA A + +PS+++ADEP
Sbjct: 111 GTDIDDKKMEERALKLLKSVNLENK-VDQKPTKLSGGERQRVAIARALVNHPSIILADEP 169

Query: 185 TSALDVVNQKVLLKVLMQMKRQGIVKSIIFITHDIATVRQIADRMIIMYAGKI 237
           T ALD   Q+V+LK+L+ + ++  V ++I +TH+    +Q ADR I +  GKI
Sbjct: 170 TGALDSETQEVILKLLLDIHKKENV-TLIMVTHEPYVAKQ-ADRSIYVLDGKI 220


Lambda     K      H
   0.321    0.138    0.405 

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: 168
Number of extensions: 8
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: 330
Length of database: 223
Length adjustment: 25
Effective length of query: 305
Effective length of database: 198
Effective search space:    60390
Effective search space used:    60390
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: 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