GapMind for catabolism of small carbon sources

 

Alignments for a candidate for natB in Pseudomonas fluorescens FW300-N1B4

Align NatB, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized)
to candidate Pf1N1B4_1382 Branched-chain amino acid ABC transporter, amino acid-binding protein (TC 3.A.1.4.1)

Query= TCDB::Q8YVY4
         (441 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1382
          Length = 377

 Score =  106 bits (264), Expect = 1e-27
 Identities = 104/343 (30%), Positives = 149/343 (43%), Gaps = 20/343 (5%)

Query: 56  LKIGSLLPATGDLASIGQQMAAAVPLVVETVNACGGVNGQPVSLVAVDDQTDPKAGAAGM 115
           +KIG   P TG  A+ G+Q         + VNA GGVNG+ + LV  DD  +PK  A  +
Sbjct: 29  IKIGVAGPMTGANAAFGEQYMKGAQAAADAVNAAGGVNGEKIVLVKGDDACEPKQ-AVTV 87

Query: 116 TKLATVDKVAGVVGSFASSVSTAAVSIAAQNKVLLISPGSTSPVFTEKAQKGDFNGFWAR 175
            K  T  KVAGVVG F SS +  A  I  +  ++ I+PGST+P  TE+     F     R
Sbjct: 88  AKDLTNQKVAGVVGHFCSSSTIPASEIYDEAGIIAITPGSTNPAVTERGLSAMF-----R 142

Query: 176 TVPPDSYQGPALAE-LANKKGFKRVSTIVINNDYGVGFEKAFVQAFEKLGGTVVNKNNPV 234
               D  QG    + + +    K+V  +   + YG G   A      K G T V      
Sbjct: 143 MCGRDDQQGIVAGDYIVDVLKGKKVVVLHDKDTYGQGLADATKAQLAKRGVTPVLYEGLT 202

Query: 235 RYDPKATTFETEAAAAFAGKPDAVLGVFYVETGSLLLKSAYQQGVAQGVQIMLTDGMKSD 294
           R +   +T  T+     AG      G  + E G  L++   +QG+ + V+ M  DG+ +D
Sbjct: 203 RGEKDFSTIVTKIRG--AGADVVYFGGLHPEAGP-LVRQLREQGL-KDVKFMSDDGIVTD 258

Query: 295 EFPAQVGKTADGKFIASGIIGTVPGSDGKGLEALTKLWQS--KKGSAPGEFAPQAWDATA 352
           E       TA G     G++ T  G+D + L     +     KKG+ P  +   A+ +  
Sbjct: 259 ELVT----TAGGPQFVDGVLMTF-GADPRLLPDSKTVVDDFRKKGTEPEGYTLYAYASVQ 313

Query: 353 LLVLAAQAAKENTGVGIAG--KIRDVSSAPGVEVTDVCEGLKL 393
            L  A   AK N G   A   K   V +  G +  D    LK+
Sbjct: 314 TLAAAFNGAKSNKGEEAAAWLKKNPVKTVMGEKTWDSKGDLKI 356


Lambda     K      H
   0.312    0.130    0.367 

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: 360
Number of extensions: 18
Number of successful extensions: 3
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: 441
Length of database: 377
Length adjustment: 31
Effective length of query: 410
Effective length of database: 346
Effective search space:   141860
Effective search space used:   141860
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Sep 17 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