GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livH in Pseudomonas putida KT2440

Align High-affinity branched-chain amino acid transport system permease protein BraD, component of Branched chain amino acid uptake transporter. Transports alanine (characterized)
to candidate PP_1140 PP_1140 branched chain amino acid transporter - permease subunit

Query= TCDB::P21627
         (307 letters)



>FitnessBrowser__Putida:PP_1140
          Length = 307

 Score =  504 bits (1299), Expect = e-148
 Identities = 255/307 (83%), Positives = 279/307 (90%)

Query: 1   MPEIYHYLQQLVNGLTVGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSYIAFIAITLL 60
           MPEIYH+ QQLVNGLT+GSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSY+AFIA+  L
Sbjct: 1   MPEIYHFFQQLVNGLTIGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSYVAFIALAGL 60

Query: 61  AMMGLDSVPLMMLAAFAASIIVTSAFGYSIERVAYRPLRGGNRLIPLISAIGMSIFLQNA 120
           AMMG+ S+P++M  AF A+I VTSA+GYSIERVAYRPLR  NRLIPLISAIGMSIFLQN 
Sbjct: 61  AMMGIHSLPILMTVAFVATIFVTSAYGYSIERVAYRPLRNSNRLIPLISAIGMSIFLQNT 120

Query: 121 VMLSQDSKEKAIPTLLPGNFVFGESSMNGVVISYMQILIFVVTFLVMFGLTLFISRSRLG 180
           V+LSQDSK+K+IP L+PG+F FG      V+ISYMQIL+FVVT + M  LTLFISRSRLG
Sbjct: 121 VLLSQDSKDKSIPNLIPGSFSFGPGGAEEVLISYMQILVFVVTLVAMTLLTLFISRSRLG 180

Query: 181 RACRACAEDLKMTNLLGINSNNIIALTFVIGAALAAVAAVLLGMQYGVINPGIGFLAGIK 240
           RACRACAED+KM NLLGIN+NNIIALTFVIGAALAAVAAVLL MQYGVINP  GFL G+K
Sbjct: 181 RACRACAEDIKMANLLGINTNNIIALTFVIGAALAAVAAVLLSMQYGVINPNAGFLVGLK 240

Query: 241 AFTAAVLGGIGSIPGAMLGGLLLGVAEAFGADVFGDQYKDVVAFGLLILVLLFRPTGILG 300
           AFTAAVLGGIGSIPGAMLGGL+LGVAEAFGAD+FGDQYKDVVAFGLL+LVLLFRPTGILG
Sbjct: 241 AFTAAVLGGIGSIPGAMLGGLVLGVAEAFGADIFGDQYKDVVAFGLLVLVLLFRPTGILG 300

Query: 301 RPEVEKV 307
           RPEVEKV
Sbjct: 301 RPEVEKV 307


Lambda     K      H
   0.328    0.145    0.413 

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: 467
Number of extensions: 9
Number of successful extensions: 1
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: 307
Length of database: 307
Length adjustment: 27
Effective length of query: 280
Effective length of database: 280
Effective search space:    78400
Effective search space used:    78400
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 48 (23.1 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