GapMind for catabolism of small carbon sources

 

Alignments for a candidate for TM0030 in Methanococcus aeolicus Nankai-3

Align TM0030, 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_011973229.1 MAEO_RS02540 ABC transporter permease

Query= TCDB::Q9WXN7
         (338 letters)



>NCBI__GCF_000017185.1:WP_011973229.1
          Length = 314

 Score =  156 bits (394), Expect = 7e-43
 Identities = 102/329 (31%), Positives = 166/329 (50%), Gaps = 21/329 (6%)

Query: 6   MFKYLLRRFIFLLVTYIVATTIVFILPRAIPGNPLSQILSGLSRVAQANPEAIRAAERTL 65
           M  ++LRR    +   I  + I F L    PGNP   IL   S  +  +  AI+  E+ L
Sbjct: 1   MKNFILRRLFLAIPMAIAVSLISFSLLYFSPGNPAEIILEQKSPDSSPDENAIKEYEKKL 60

Query: 66  MEEFGLGKPWYVQYFEFITKALRGDLGTSITFYPRKVIDLIIPVIPWTLILLLPATIVAW 125
               GL KP+Y  Y  +++KAL GD G S+      VID  +   P+T+++++ AT V +
Sbjct: 61  ----GLDKPFYDLYVIWLSKALTGDFGVSLQ-NGEPVIDEFMARFPYTVMIMVGATTVYF 115

Query: 126 ILGNSLGALAAYKRNTWIDKGVLTTSLIVSQIPYYWLGMIFIFLFGVKLGWLPVQGAYSQ 185
           +LG  +G L+A  ++  ID  V   + +   IP +WL ++ I++F VKL           
Sbjct: 116 VLGVVMGILSALNKDGIIDNIVRAYASLKMAIPSFWLALLLIWVFSVKL----------- 164

Query: 186 GTIPNLSWSFFVDVLKHYIMPFASIVVSAMGGWAIGMRLMVIYELGSDYAMFSEYLGMKD 245
                +  +F  + L   I+P  ++ +   G  A  +R  ++  + SDY + +   G+ +
Sbjct: 165 ----KIISAFGYNGLDSLILPSFALGLGMAGSLARVLRTCILEVMSSDYILTARAKGLSN 220

Query: 246 KRI-FKYVFRNSLLPQITGLALSLGGVLGGALITEIVFNYPGTGYLLFRALTTLDYPLIQ 304
           K +  K+V +N+ LP IT + +    +LGGA+I E +F +PG G      +   DYP + 
Sbjct: 221 KVVVLKHVLKNAFLPVITLMGMKTAYLLGGAVIIESIFGWPGIGSYFIDIINAKDYPAVS 280

Query: 305 GIFVILIASIYLANFIVDFLYALIDPRIR 333
           G+  I      L N IVD  YA++DPR+R
Sbjct: 281 GLVFIFGILFVLVNLIVDISYAILDPRVR 309


Lambda     K      H
   0.329    0.146    0.449 

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: 336
Number of extensions: 26
Number of successful extensions: 6
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: 314
Length adjustment: 28
Effective length of query: 310
Effective length of database: 286
Effective search space:    88660
Effective search space used:    88660
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 48 (23.1 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