GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Pf6N2E2_5402 in Rhodobacter viridis JA737

Align ABC transporter for D-Alanine, periplasmic substrate-binding component (characterized)
to candidate WP_110804792.1 C8J30_RS05885 amino acid ABC transporter substrate-binding protein

Query= reanno::pseudo6_N2E2:Pf6N2E2_5402
         (343 letters)



>NCBI__GCF_003217355.1:WP_110804792.1
          Length = 338

 Score =  333 bits (853), Expect = 5e-96
 Identities = 167/340 (49%), Positives = 223/340 (65%), Gaps = 2/340 (0%)

Query: 4   LKSTLAVMTAAAVLGVSGFAQAGATLDAVQKKGFVQCGVSDGLPGFSVPDSTGKIVGIDA 63
           +K ++   T A V  V+G A A +TLD V+ +G + CGV+ GL GF  PD+ G   G D 
Sbjct: 1   MKKSVFFGTVALVALVAGAASA-STLDDVKARGQLICGVNPGLTGFGAPDANGNYQGFDV 59

Query: 64  DFCRAVAAAVFGDATKVKFSQLNAKERFTALQSGEIDMLSRNSTMTSSRDAGMGLKFPGF 123
             C+AVAAAV GD  KV++  L  + RFTAL SGE+DML+RNST T  RD  + L F   
Sbjct: 60  AACKAVAAAVLGDPMKVQYKALTGETRFTALASGEVDMLARNSTWTFGRDTELALDFVA- 118

Query: 124 ITYYDGIGFLANNKLGVKSAKELDGATICIQAGTTTELNVSDYFRANGLKYTPITFDTSD 183
           + YYDG GF+ N  LGV SAKELDGAT+C+Q GTTTE+N++DYF++N + YTP+      
Sbjct: 119 VNYYDGQGFMVNKSLGVSSAKELDGATVCVQTGTTTEMNLADYFKSNNMTYTPVNIADDA 178

Query: 184 ESAKSLESGRCDVLTSDKSQLFAQRSKLASPKDYVVLPETISKEPLGPVVRNGDDEWLAI 243
           E  +   +G CD  T+D S L A R+ + +  D V+LPE ISKEPL   VR+GD+ W  I
Sbjct: 179 EGQQKFLAGACDSYTTDASGLAASRATMPNAADIVILPEIISKEPLALAVRHGDNNWGDI 238

Query: 244 VRWTGYALLNAEEAGVTSKNVEAEAKSTKNPDVARMLGADGEYGKDLKLPKDWVVQIVKQ 303
           VRW+ YAL+ AEE G+T  N+E  A ST+NP++ R+LG +G+ GK + L  D+  + +  
Sbjct: 239 VRWSFYALVAAEEYGITKANLEEVAASTQNPEIRRLLGLEGDMGKKIGLDNDFAKRAIMA 298

Query: 304 VGNYGEMFERNLGKGTPLEIDRGLNALWNAGGIQYAPPVR 343
            GNYGE+FE N+G  T + + RGLNA W  GG+ YAPP R
Sbjct: 299 SGNYGEIFEANIGASTSIGLARGLNAQWTQGGLMYAPPFR 338


Lambda     K      H
   0.315    0.133    0.383 

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: 14
Number of successful extensions: 2
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: 343
Length of database: 338
Length adjustment: 28
Effective length of query: 315
Effective length of database: 310
Effective search space:    97650
Effective search space used:    97650
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: 49 (23.5 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