GapMind for catabolism of small carbon sources

 

Alignments for a candidate for TM1749 in Methanobacterium lacus AL-21

Align TM1749, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (characterized)
to candidate WP_013645374.1 METBO_RS08905 ABC transporter ATP-binding protein

Query= TCDB::Q9X271
         (324 letters)



>NCBI__GCF_000191585.1:WP_013645374.1
          Length = 223

 Score =  114 bits (286), Expect = 2e-30
 Identities = 77/230 (33%), Positives = 132/230 (57%), Gaps = 15/230 (6%)

Query: 4   LLNVNNLKVEFHRVEGIVKAVDGISYKLNKGESLGIVGESGSGKSVSVLSLLRLINRNGR 63
           ++ + NLK E+   +G + A++ +  ++ +GES+ I+G SGSGKS    +LL +I    +
Sbjct: 6   IIKIKNLKKEYE--DGSIIALNNVDLEIERGESVSIIGPSGSGKS----TLLNMIGGLDK 59

Query: 64  IVDGEAIFLGKDLLKLNKEELRNIRGKDISIIFQNPMTSLNPIIRVGIQVMEPIIWHRLM 123
             +G+    G +L+  +  +L N R  +I  +FQ  + +L P + V   V  P++   + 
Sbjct: 60  ANEGQISVAGVNLM--DNSDLSNFRSNEIGFVFQ--LHNLIPNLTVLENVQIPLLGTDI- 114

Query: 124 KNEEARERAIELLERVGIPESPKRFLNYPFQFSGGMRQRVMIAMALACHPKLLIADEPTT 183
            +++  ERA++LL+ V +     +    P + SGG RQRV IA AL  HP +++ADEPT 
Sbjct: 115 DDKKMEERALKLLKSVNLENKVDQ---KPTKLSGGERQRVAIARALVNHPSIILADEPTG 171

Query: 184 ALDVTIQAQIMELLQELKEEYGMSVIFITHDLSVATNFCDRIITMYAGKI 233
           ALD   Q  I++LL ++ ++  +++I +TH+  VA    DR I +  GKI
Sbjct: 172 ALDSETQEVILKLLLDIHKKENVTLIMVTHEPYVAKQ-ADRSIYVLDGKI 220


Lambda     K      H
   0.320    0.139    0.401 

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: 158
Number of extensions: 11
Number of successful extensions: 1
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: 324
Length of database: 223
Length adjustment: 25
Effective length of query: 299
Effective length of database: 198
Effective search space:    59202
Effective search space used:    59202
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