GapMind for catabolism of small carbon sources

 

Alignments for a candidate for cbtD in Ochrobactrum thiophenivorans DSM 7216

Align CbtD, component of Cellobiose and cellooligosaccharide porter (characterized)
to candidate WP_094506802.1 CEV31_RS09385 ABC transporter ATP-binding protein

Query= TCDB::Q97VF5
         (362 letters)



>NCBI__GCF_002252445.1:WP_094506802.1
          Length = 610

 Score =  179 bits (453), Expect = 2e-49
 Identities = 106/290 (36%), Positives = 170/290 (58%), Gaps = 12/290 (4%)

Query: 45  ILEVHNLNVIYDEGNSRIIKAVNDVSFGVEKGEILGIIGESGSGKTTLISAILRAIRPPG 104
           +L + NL+V +  G++R+   V+D+SF V  G  L ++GESGSGK+    +I+R     G
Sbjct: 9   LLNIENLSVEF--GSNRV---VDDLSFSVSPGRTLAVVGESGSGKSITSLSIMRLADVSG 63

Query: 105 -KIISGKVIFNG----MDIFSMTIDEFRKLLWKDISYVPQASQNALNPVLPISEIFYHEA 159
            K  +G+++FNG     D+        R +  KDI+ + Q    +LNPV  I        
Sbjct: 64  AKFPTGRILFNGPDGERDLLKADQKTMRGIRGKDIAMIFQEPMTSLNPVFTIGNQLSEVL 123

Query: 160 ISHGEADKKRVIERASELLKLVGLDPAR-VLKMYPFQLSGGMKQRVMIALSLLLNPKLIL 218
           + H    K   +     LL++V L  A  +LK YP QLSGGM+QRVMIA++L   PKL++
Sbjct: 124 MLHEGLSKTASLAEGKRLLEMVRLPDAEGLLKRYPHQLSGGMRQRVMIAMALACRPKLLI 183

Query: 219 MDEPTSALDMLNQELLLKLIKNINQEMGVTIVYVTHDILNIAQIANRLLVMYKGYVMEEG 278
            DEPT+ALD+  Q  +L +IK++ +E+ + ++++THD+  +A++A+ ++VM+KG  +EEG
Sbjct: 184 ADEPTTALDVTIQAQILHIIKDLQKELEMAVIFITHDMGVVAEMADDVVVMWKGKKVEEG 243

Query: 279 KTEEIIKSPLNPYTSLLVSSIPSLKGEVKVINVPLDEPLVSKEKGCPFLA 328
               I ++P +PYT  L+SS+P L G +     P   P++    G P L+
Sbjct: 244 PVGRIFEAPQHPYTQTLLSSVPKL-GSMTGEAFPKRMPVMMMRDGVPVLS 292



 Score =  144 bits (364), Expect = 5e-39
 Identities = 81/242 (33%), Positives = 140/242 (57%), Gaps = 7/242 (2%)

Query: 60  SRIIKAVNDVSFGVEKGEILGIIGESGSGKTTLISAILRAIRPPGKIISGKVIFNGMDIF 119
           + +  AV+ V+F +  GE L ++GESGSGK+T+   I +   P    +SG + FNG    
Sbjct: 329 THVCNAVSKVAFDIYPGETLALVGESGSGKSTIGRTIQQLQSP----LSGDIRFNGKAYS 384

Query: 120 SMTIDEFRKLLWKDISYVPQASQNALNPVLPISEIFYHEAISHGEADKKRVIE-RASELL 178
            M+  E  K+  +++ Y+ Q    +L+P   +         +HG  D  + I  R +ELL
Sbjct: 385 QMSSSERYKMR-REVQYIFQDPFASLDPRKTVGFSIAEPIRTHGLLDNNKAINARVAELL 443

Query: 179 KLVGLDPARVLKMYPFQLSGGMKQRVMIALSLLLNPKLILMDEPTSALDMLNQELLLKLI 238
           + VGL P    + YP + SGG +QR+ IA +L   PKLI+ DE  SALD+  Q  ++ L 
Sbjct: 444 ERVGLGPEHASR-YPHEFSGGQRQRICIARALASKPKLIIADEALSALDVSIQAQVINLF 502

Query: 239 KNINQEMGVTIVYVTHDILNIAQIANRLLVMYKGYVMEEGKTEEIIKSPLNPYTSLLVSS 298
            ++ +E G+  ++++HD+  + ++++R+ V+Y G +ME G   ++ ++P +PYT  L+S+
Sbjct: 503 MDLQKEQGLAYLFISHDMAVVEKMSHRVAVLYLGQIMELGSRRQVFETPSHPYTQRLLSA 562

Query: 299 IP 300
           +P
Sbjct: 563 VP 564


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: 23
Number of successful extensions: 5
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: 610
Length adjustment: 33
Effective length of query: 329
Effective length of database: 577
Effective search space:   189833
Effective search space used:   189833
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