GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braE in Dinoroseobacter shibae DFL-12

Align High-affinity branched-chain amino acid transport system permease protein BraE, component of Branched chain amino acid uptake transporter. Transports alanine (characterized)
to candidate 3608584 Dshi_1978 inner-membrane translocator (RefSeq)

Query= TCDB::P21628
         (417 letters)



>FitnessBrowser__Dino:3608584
          Length = 317

 Score =  142 bits (357), Expect = 2e-38
 Identities = 100/316 (31%), Positives = 151/316 (47%), Gaps = 42/316 (13%)

Query: 114 VDIATLILIYVMLGIGLNIVVGLAGLLDLGYVGFYAVGAYTYALL------AEYAGFGFW 167
           V  AT+  I  +  +GLN+  G  GL + G V F+  G Y   +L      A   GFG  
Sbjct: 9   VFFATIASILAIAVLGLNLHWGNTGLFNGGVVAFFGAGGYATLILGGTPQAAHLGGFGLP 68

Query: 168 TALPIAG--MMAALFGFLLGFPVLRLRGDYLAIVTLGFGEIIRILLRNMTEITGGPNGIG 225
             L + G  ++A L  +L+G   +RLR DYLAI T G       L+RN   + GG +G+ 
Sbjct: 69  YGLALLGGLVIAGLLAWLVGLLTIRLRHDYLAIATFGVAVAFENLVRNAQRLAGGASGLR 128

Query: 226 SIPKPTLFGLTFERRAPEGMQTFHEFFGIAYNTNYKVILLYVVALLLVLLALFVINRLMR 285
                      FER   + +       G+AYN  +   +L   AL+   L L    RL+R
Sbjct: 129 G----------FERPLADTIPP-----GLAYNAAFFAFVL--AALIATYLGL---ERLIR 168

Query: 286 MPIGRAWEALREDEVACRALGLNPTIVKLSAFTIGASFAGFAGSFFAARQGLVTPESFTF 345
            P GR   A+REDE A RALG +P  ++L+AF IG+   G AG+ +A     ++P+    
Sbjct: 169 GPFGRLLRAIREDETAARALGKSPDRIRLTAFVIGSVILGLAGALYATFYAFISPQDVLP 228

Query: 346 IESAMILAIVVLGGMGSQLGVILAAVVMVLLQEMRGF--------------NEYRMLIFG 391
           I +  I A++++GG G+  G I  A ++       G+                 + ++ G
Sbjct: 229 ILTFQIWAMLIVGGAGNNRGAIAGAFLIWGAWTASGWALSRFAPIEVQLYTGSIQFVLIG 288

Query: 392 LTMIVMMIWRPQGLLP 407
             ++ M++WRPQGL P
Sbjct: 289 CVIVGMLLWRPQGLFP 304


Lambda     K      H
   0.330    0.146    0.439 

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: 420
Number of extensions: 23
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: 417
Length of database: 317
Length adjustment: 29
Effective length of query: 388
Effective length of database: 288
Effective search space:   111744
Effective search space used:   111744
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 49 (23.5 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