GapMind for catabolism of small carbon sources

 

Alignments for a candidate for tctC in Dinoroseobacter shibae DFL-12

Align Tricarboxylate transport protein TctC (characterized)
to candidate 3607812 Dshi_1220 hypothetical protein (RefSeq)

Query= reanno::Dino:3609740
         (326 letters)



>FitnessBrowser__Dino:3607812
          Length = 328

 Score =  115 bits (289), Expect = 1e-30
 Identities = 99/331 (29%), Positives = 147/331 (44%), Gaps = 13/331 (3%)

Query: 1   MTLEFTRRTL--IAAAAALAMTGGAHAEGE-QMLESIHFLIPGGAGGGWDGTARGTGEAL 57
           MTL FTRR    IA AAA ++   A A+ + +  + I  +I  G GGG D  AR     +
Sbjct: 1   MTLNFTRRVALTIATAAATSIALPAFADDDWKPNKPIEMVIMAGQGGGADRLARLFQSII 60

Query: 58  TKAGLVGSASYE-NMSGGGGGKAIAYLIENANSSHGTLMVNSTPIVIRSLTGEISQSFRD 116
            K  L        N  GG G +A+ YL +    SH  +M          +  +I     +
Sbjct: 61  QKENLASMPVLPVNKGGGSGAEALRYLKDKEGDSH-VIMATLNSYYTTPIRTDIGVDIEE 119

Query: 117 LTLVAGTIGDYAAIVVGKDSPINSMADLIAAYDADPNATAVGGGSVPGGMDHLVAAMVME 176
            T +A    D   + V  DS I ++ D +AA +A   A  +GG    G  D LV AM+ +
Sbjct: 120 FTPLARMALDTFVLWVNADSDIYTLEDYVAAVNASGGAWKMGGTGT-GQEDSLVTAMLEK 178

Query: 177 AAGKDALGVKYIPYDAGGKAMAALLSGEIAALSTGFSEAIDLAEAGEVKIIGVTAPERVA 236
             G   +   Y+P++ GG     L+ G I +     SEA+   +AG+V+ I    PER+A
Sbjct: 179 EFG---IKHTYVPFNGGGTVAKNLVGGHIDSTVNNPSEAMGFWQAGKVRPIAAFTPERLA 235

Query: 237 AYDSAPTMVEQGIDTTFVNW--RGFFAAPGLPEEQLAAYQATLEKMYDTPEWEEVRARNG 294
            +   PT  E G + + V W  R F     +P E +A Y A  E +  T EW+       
Sbjct: 236 VFPDVPTATELGHE-SLVYWMQRSFVGPKDMPAEAVAYYTAMFEGLAQTEEWQTYTQEKA 294

Query: 295 WVNIHNSGADFQS-FLEAQEAQIGDLMKKLG 324
            +    +G   Q+ FLE ++     L +  G
Sbjct: 295 LMADFLTGDALQAYFLEERDKHAAILQEMEG 325


Lambda     K      H
   0.315    0.132    0.378 

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: 298
Number of extensions: 18
Number of successful extensions: 5
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: 326
Length of database: 328
Length adjustment: 28
Effective length of query: 298
Effective length of database: 300
Effective search space:    89400
Effective search space used:    89400
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 48 (23.1 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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