GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braC in Pseudomonas putida KT2440

Align Leucine-, isoleucine-, valine-, threonine-, and alanine-binding protein; LIVAT-BP; Leu/Ile/Val/Thr/Ala-binding protein (characterized)
to candidate PP_4867 PP_4867 branched-chain amino acid ABC transporter, periplasmic amino acid-binding protein (braC-like)

Query= SwissProt::P21175
         (373 letters)



>FitnessBrowser__Putida:PP_4867
          Length = 378

 Score =  285 bits (728), Expect = 2e-81
 Identities = 154/361 (42%), Positives = 225/361 (62%), Gaps = 10/361 (2%)

Query: 12  FAAMAIA---GFASYSMAADTIKIALAGPVTGPVAQYGDMQRAGALMAIEQINKAGGVNG 68
           F A+A+A   G +SY  A   +KI +AGP+TG  A +G+    GA  A ++IN AGGVNG
Sbjct: 10  FLALAVATALGVSSYVQA--DVKIGVAGPMTGANAAFGEQYMKGAQAAADKINAAGGVNG 67

Query: 69  AQLEGVIYDDACDPKQAVAVANKVVN-DGVKFVVGHVCSSSTQPATDIYEDEGVLMITPS 127
            ++  V  DDAC+PKQAVAVAN++V+ D V  VVGH CSS+T PA+++Y++ GV+ ITP 
Sbjct: 68  EKIVLVKGDDACEPKQAVAVANRLVDQDKVIGVVGHFCSSNTIPASEVYDEAGVIAITPG 127

Query: 128 ATAPEITSRGYKLIFRTIGLDNMQGPVAGKFIAERYKDKTIAVLHDKQQYGEGIATEVKK 187
           +T P++T RG   +FR  G D+ QG VAG +I +  K K +AVLHDK  YG+G+A   K 
Sbjct: 128 STNPQVTERGLSAMFRMCGRDDQQGIVAGDYIVDVLKGKKVAVLHDKDTYGQGLADATKA 187

Query: 188 TVEDAGIKVAVFEGLNAGDKDFNALISKLKKAGVQFVYFGGYHPEMGLLLRQAKQAGL-D 246
            +E  G+K  ++EGL  G+KDF+A+++K++  G   VYFGG HPE G L+RQ ++ GL D
Sbjct: 188 QLEKRGVKPVLYEGLTRGEKDFSAVVTKIRSTGADVVYFGGLHPEAGPLVRQLREQGLKD 247

Query: 247 ARFMGPEGVGNSEITAIAGDAS--EGMLATLPRAFEQDPKNKALIDAFKAKNQDPSGIFV 304
            +FM  +G+   E+ + AG A   +G+  T        P +KA+++ F+    +P G + 
Sbjct: 248 VKFMSDDGIVTDELVSTAGGAQYVDGVYMTFGADPRLLPDSKAVVEEFRKAGTEPEG-YT 306

Query: 305 LPAYSAVTVIAKGIEKAGEADPEKVAEALRANTFETPTGNLGFDEKGDLKNFDFTVYEWH 364
           L AY+++  +A     A     E  A+ L+AN  +T  G   +D KGDL   D+ VY+W 
Sbjct: 307 LYAYASLQALAAAFNGAKSNKGEDAAKWLKANPVQTVMGEKKWDSKGDLTVSDYVVYQWD 366

Query: 365 K 365
           K
Sbjct: 367 K 367


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: 407
Number of extensions: 15
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: 378
Length adjustment: 30
Effective length of query: 343
Effective length of database: 348
Effective search space:   119364
Effective search space used:   119364
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.

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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