GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braD in Pseudomonas fluorescens FW300-N2C3

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 AO356_05325 AO356_05325 branched-chain amino acid transporter permease subunit LivH

Query= TCDB::P21627
         (307 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_05325
          Length = 307

 Score =  517 bits (1331), Expect = e-151
 Identities = 259/307 (84%), Positives = 284/307 (92%)

Query: 1   MPEIYHYLQQLVNGLTVGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSYIAFIAITLL 60
           MP+IYH+ QQLVNGLTVGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSY+AFIAI  L
Sbjct: 1   MPDIYHFFQQLVNGLTVGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSYVAFIAIAGL 60

Query: 61  AMMGLDSVPLMMLAAFAASIIVTSAFGYSIERVAYRPLRGGNRLIPLISAIGMSIFLQNA 120
           +MMGLDSVPL+M AAF ASI+VTS++GYSIER+AYRPLRG NRLIPLISAIGMSIFLQN 
Sbjct: 61  SMMGLDSVPLLMTAAFLASIVVTSSYGYSIERIAYRPLRGSNRLIPLISAIGMSIFLQNT 120

Query: 121 VMLSQDSKEKAIPTLLPGNFVFGESSMNGVVISYMQILIFVVTFLVMFGLTLFISRSRLG 180
           V+LSQDSK+K+IP L+PGNF  G    + V+ISYMQI++FVVT + M GLTLFISRSRLG
Sbjct: 121 VLLSQDSKDKSIPNLIPGNFAIGPGGAHEVLISYMQIVVFVVTLVAMLGLTLFISRSRLG 180

Query: 181 RACRACAEDLKMTNLLGINSNNIIALTFVIGAALAAVAAVLLGMQYGVINPGIGFLAGIK 240
           RACRACAED+KM NLLGIN+NNIIALTFVIGAALAA+AAVLL MQYGVINP  GFL G+K
Sbjct: 181 RACRACAEDIKMANLLGINTNNIIALTFVIGAALAAIAAVLLSMQYGVINPNAGFLVGLK 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: 470
Number of extensions: 10
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