GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braC in Pseudomonas fluorescens FW300-N2E3

Align Leucine-, isoleucine-, valine-, threonine-, and alanine-binding protein; LIVAT-BP; Leu/Ile/Val/Thr/Ala-binding protein (characterized)
to candidate AO353_13340 AO353_13340 amino acid ABC transporter substrate-binding protein

Query= SwissProt::P21175
         (373 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_13340
          Length = 377

 Score =  280 bits (715), Expect = 6e-80
 Identities = 152/358 (42%), Positives = 217/358 (60%), Gaps = 9/358 (2%)

Query: 12  FAAMAIA---GFASYSMAADTIKIALAGPVTGPVAQYGDMQRAGALMAIEQINKAGGVNG 68
           F A+A+A   G +S+  A   +K+ +AGP+TGP A +G     GA  A + IN  GG+NG
Sbjct: 10  FVALAVAAALGVSSFVQA--DVKLGVAGPMTGPSASFGLQYMKGAQAAADAINAKGGING 67

Query: 69  AQLEGVIYDDACDPKQAVAVANKVVNDGVKFVVGHVCSSSTQPATDIYEDEGVLMITPSA 128
            ++  V  DDAC+PKQAVAVANK+V D V  VVGH CSSST PA+++Y D G++ ITP +
Sbjct: 68  EKIVLVQGDDACEPKQAVAVANKMVQDKVIGVVGHFCSSSTIPASEVYSDAGIIAITPGS 127

Query: 129 TAPEITSRGYKLIFRTIGLDNMQGPVAGKFIAERYKDKTIAVLHDKQQYGEGIATEVKKT 188
           T P +T RG   + R  G D+ QG VAG +I +  K K +AV++DK  YG+G+A    K 
Sbjct: 128 TNPTVTERGLPAMMRMCGRDDQQGIVAGNYIVDVLKGKKVAVINDKDTYGKGLADATAKQ 187

Query: 189 VEDAGIKVAVFEGLNAGDKDFNALISKLKKAGVQFVYFGGYHPEMGLLLRQAKQAGL-DA 247
           +   G+K  + EGL  G+KDF+ALI+K++  G   +YFGG HPE G L+ Q ++ GL D 
Sbjct: 188 LTARGVKPVLEEGLTRGEKDFSALITKVRSVGADVLYFGGLHPEAGPLVHQLREQGLKDV 247

Query: 248 RFMGPEGVGNSEITAIAGDAS--EGMLATLPRAFEQDPKNKALIDAFKAKNQDPSGIFVL 305
           +FM  +G+   E+   AG A   +G+  T        P +KA++D F+    +P G + L
Sbjct: 248 KFMSDDGIVTDEMVTTAGGAPYVDGVYMTFGADPRLIPDSKAVVDTFRKSGYEPEG-YTL 306

Query: 306 PAYSAVTVIAKGIEKAGEADPEKVAEALRANTFETPTGNLGFDEKGDLKNFDFTVYEW 363
            AY++V  +A G   A     E+ A+ L+A+  ET  G   +D KGDLK  D+ VY+W
Sbjct: 307 YAYASVQALAAGFNGAKSNKGEEAAKWLKAHPVETVMGKKEWDSKGDLKISDYVVYQW 364


Lambda     K      H
   0.316    0.133    0.377 

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: 396
Number of extensions: 27
Number of successful extensions: 4
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: 373
Length of database: 377
Length adjustment: 30
Effective length of query: 343
Effective length of database: 347
Effective search space:   119021
Effective search space used:   119021
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: 41 (21.6 bits)
S2: 50 (23.9 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