GapMind for catabolism of small carbon sources

 

Alignments for a candidate for cbtD in Flavobacterium beibuense F44-8

Align CbtD, component of Cellobiose and cellooligosaccharide porter (characterized)
to candidate WP_035131541.1 Q763_RS04180 ABC transporter ATP-binding protein

Query= TCDB::Q97VF5
         (362 letters)



>NCBI__GCF_000769915.1:WP_035131541.1
          Length = 562

 Score =  175 bits (444), Expect = 2e-48
 Identities = 95/249 (38%), Positives = 155/249 (62%), Gaps = 12/249 (4%)

Query: 66  VNDVSFGVEKGEILGIIGESGSGKTTLISAILRAIRPPG--KIISGKVIFNGMDIFSMTI 123
           V+D +F +E+ EILGI+GESGSGK+    A++  + P G  ++  G + F G DI  +T 
Sbjct: 25  VHDSTFTLEQNEILGIVGESGSGKSVTSLAVM-GLLPKGILQVTQGSIAFEGRDISQLTT 83

Query: 124 DEFRKLLWKDISYVPQASQNALNPVLP----ISEIFYHEAISHGEADKKRVIERASELLK 179
            E R +   DI+ + Q   ++LNP L     + EIF      H    K+ +      L +
Sbjct: 84  REMRNIRGNDIAMIFQEPMSSLNPSLKCGYQVEEIFKE----HTSLSKREIKATVLSLFE 139

Query: 180 LVGL-DPARVLKMYPFQLSGGMKQRVMIALSLLLNPKLILMDEPTSALDMLNQELLLKLI 238
            V L +P ++   YP ++SGG KQRVMIA+++   PK+++ DEPT+ALD+  Q+ ++ L+
Sbjct: 140 KVKLPNPEKIYNRYPHEISGGQKQRVMIAMAIACKPKILIADEPTTALDVTVQKEIILLL 199

Query: 239 KNINQEMGVTIVYVTHDILNIAQIANRLLVMYKGYVMEEGKTEEIIKSPLNPYTSLLVSS 298
           K + QE  ++I++++HD+  +++IANR+LVMYKG ++E+G   EI ++P + YT  L++S
Sbjct: 200 KELQQETKMSIIFISHDLSLVSEIANRVLVMYKGNIVEQGVATEIFENPKHTYTKALINS 259

Query: 299 IPSLKGEVK 307
            PSL   +K
Sbjct: 260 RPSLDVRLK 268



 Score =  148 bits (374), Expect = 3e-40
 Identities = 91/263 (34%), Positives = 149/263 (56%), Gaps = 14/263 (5%)

Query: 45  ILEVHNLNVIYDE-----GNSRIIKAVNDVSFGVEKGEILGIIGESGSGKTTLISAILRA 99
           +LEV N+   Y       G     KAVN+VSF + +GE LG++GESG GK+TL +AIL+ 
Sbjct: 304 LLEVINVEKEYVSSSGLFGRDVKFKAVNNVSFKIYEGETLGLVGESGCGKSTLGNAILQL 363

Query: 100 IRPPGKIISGKVIFNGMDIFSMTIDEFRKLLWKDISYVPQASQNALNPVLPISEIFYHEA 159
                K  +G +++ G D+  ++    R+L  K+I  + Q   ++LNP + + +      
Sbjct: 364 ----DKATAGSILYKGQDLTKLSASAIRELR-KEIQIIFQDPYSSLNPRITVGKAIMEPM 418

Query: 160 ISHG--EADKKRVIERASELLKLVGLDPARVLKMYPFQLSGGMKQRVMIALSLLLNPKLI 217
             HG  + D++R  E+  E+LK VGL        YP + SGG +QRV IA ++ L PKLI
Sbjct: 419 KVHGLYKNDRERR-EKTIEILKRVGLGEEH-FNRYPHEFSGGQRQRVGIARTIALQPKLI 476

Query: 218 LMDEPTSALDMLNQELLLKLIKNINQEMGVTIVYVTHDILNIAQIANRLLVMYKGYVMEE 277
           + DE  SALD+  Q  +L L+  + +  G T ++++HD+  +  +++++LVM KG + E 
Sbjct: 477 VCDESVSALDISVQAQVLNLLNELKENFGFTYIFISHDLAVVKYMSDQVLVMNKGQIEEM 536

Query: 278 GKTEEIIKSPLNPYTSLLVSSIP 300
            + + + + P   YT  L+ +IP
Sbjct: 537 NEADALYEHPEKEYTKKLIEAIP 559


Lambda     K      H
   0.319    0.138    0.391 

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: 471
Number of extensions: 22
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 362
Length of database: 562
Length adjustment: 33
Effective length of query: 329
Effective length of database: 529
Effective search space:   174041
Effective search space used:   174041
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: 51 (24.3 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