GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braD in Limnohabitans curvus MWH-C5

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 WP_108402619.1 B9Z44_RS12860 branched-chain amino acid ABC transporter permease

Query= TCDB::P21627
         (307 letters)



>NCBI__GCF_003063475.1:WP_108402619.1
          Length = 291

 Score =  161 bits (407), Expect = 2e-44
 Identities = 102/302 (33%), Positives = 164/302 (54%), Gaps = 15/302 (4%)

Query: 7   YLQQLVNGLTVGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSYIAFIAITLLAMMGLD 66
           +LQ   +GL  GS YAL A+G+T+++   G INFA GE  M+ +++         M+G  
Sbjct: 4   FLQLFFSGLATGSIYALAALGFTLLWQASGTINFAQGEFVMLPAFM---------MLGFL 54

Query: 67  SVPLMMLAAFAASIIVTS-AFGYSIERVAYRPLRGGNRLIPLISAIGMSIFLQNAVMLSQ 125
           +    ++ +FAAS +V+    G+  +R    PL     +  +++ IG+SI ++NAV    
Sbjct: 55  AAGFPLVLSFAASCVVSVFVLGWLFKRGVVDPLFKFGMMPIVVATIGLSIAMRNAVRAGY 114

Query: 126 DSKEKAIPTLLPGNFVFGESSMNGVVISYMQILIFVVTFLVMFGLTLFISRSRLGRACRA 185
            ++    P L P        ++ GV IS   I  FV    ++     F++++  GRA +A
Sbjct: 115 SAEPHPFPNLFPDEVY----NIAGVTISATDIGTFVFAIALVLVTQAFLAKTVTGRAMQA 170

Query: 186 CAEDLKMTNLLGINSNNIIALTFVIGAALAAVAAVLLGMQYGVINPGIGFLAGIKAFTAA 245
            A++ +  ++LGIN   +I  TF I A LAA AA+L+   Y +    +G   G KAF AA
Sbjct: 171 VAQNTESASVLGINVPRMIFYTFAINALLAAAAAILVTPTY-LAKFDMGASLGNKAFFAA 229

Query: 246 VLGGIGSIPGAMLGGLLLGVAEAFGADVFGDQYKDVVAFGLLILVLLFRPTGILGRPEVE 305
           ++GG  +  GA+LGG+++GV E   A      YKD VA  + ++V+LF+P G+LG+    
Sbjct: 230 IIGGFNNSRGALLGGVIVGVCENLAAAYISPAYKDAVALVIFMVVILFKPQGLLGKKVER 289

Query: 306 KV 307
           KV
Sbjct: 290 KV 291


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: 238
Number of extensions: 9
Number of successful extensions: 5
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: 291
Length adjustment: 27
Effective length of query: 280
Effective length of database: 264
Effective search space:    73920
Effective search space used:    73920
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 24 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