GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braE in Desulfovibrio vulgaris Miyazaki F

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 8501894 DvMF_2609 inner-membrane translocator (RefSeq)

Query= TCDB::P21628
         (417 letters)



>FitnessBrowser__Miya:8501894
          Length = 415

 Score =  331 bits (849), Expect = 2e-95
 Identities = 183/407 (44%), Positives = 259/407 (63%), Gaps = 24/407 (5%)

Query: 3   QSLKRALFSALLVILVSYPILGLKLRTVGIKLEVLGADAQTLWTIAAAALAMFVWQ--LF 60
           Q LK+++  +L  + +++P++ +++ ++   ++    +   L     + +  FVW+  L 
Sbjct: 2   QGLKKSILVSLWFMFLTFPLMVIRIDSLNGTIDWRWENM--LGMGVGSFVLSFVWRFMLA 59

Query: 61  RDRIPLKLGRGVGYKVNGSGLKNFLSLPSTQRWAVLALVVVAFVWPFFASRGAVDIATLI 120
           R         G      G+  +   S P     A++ L+    V P+  S    +I    
Sbjct: 60  RKEAGRAAAAGGAMSARGAWFERLRSDPKAAVPALVVLLSAFLVLPWVVSTYQTNIMISA 119

Query: 121 LIYVMLGIGLNIVVGLAGLLDLGYVGFYAVGAYTYALLAEYAGFGFWTALPIAGMMAALF 180
           L+YVMLG+GLNIVVGL+G L LGYV FYAVGAY+YA+L    G GFW+ LPI G MAALF
Sbjct: 120 LLYVMLGLGLNIVVGLSGQLVLGYVAFYAVGAYSYAILNSNFGLGFWSVLPIGGAMAALF 179

Query: 181 GFLLGFPVLRLRGDYLAIVTLGFGEIIRILLRNMTEITGGPNGIGSIPKPTLFGLTFERR 240
           G LLGFPVLRLRGDYLAIVTLGFGEIIR++L N +  + GP+GI +I +P L G+     
Sbjct: 180 GILLGFPVLRLRGDYLAIVTLGFGEIIRLVLENWSSFSQGPSGIANIERPGLLGMQ---- 235

Query: 241 APEGMQTFHEFFGIAYNTNYKVILLYVVALLLVLLALFVINRLMRMPIGRAWEALREDEV 300
                        ++  T Y    +Y + L  V++ +  + RL    IGRAW+ALREDE+
Sbjct: 236 -----------LSVSDATTY----IYYLILAAVIVTILAVTRLKNSRIGRAWQALREDEI 280

Query: 301 ACRALGLNPTIVKLSAFTIGASFAGFAGSFFAARQGLVTPESFTFIESAMILAIVVLGGM 360
           AC+A+G++ T  KL+AF +GA +AGFAG  FAA+   + P SFTF+ESAM+LA+VVLGGM
Sbjct: 281 ACQAMGIDITTTKLTAFALGACWAGFAGVIFAAKTTFINPASFTFLESAMVLAMVVLGGM 340

Query: 361 GSQLGVILAAVVMVLLQE-MRGFNEYRMLIFGLTMIVMMIWRPQGLL 406
           GS +GV + A+V++LL E +R F+EYRMLIFG TM++MM++RPQGL+
Sbjct: 341 GSVIGVSVGALVLILLPEYLRAFSEYRMLIFGATMVLMMVFRPQGLV 387


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: 573
Number of extensions: 37
Number of successful extensions: 3
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: 415
Length adjustment: 31
Effective length of query: 386
Effective length of database: 384
Effective search space:   148224
Effective search space used:   148224
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: 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