GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braD in Marinobacter adhaerens HP15

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 GFF2762 HP15_2706 inner-membrane translocator

Query= TCDB::P21627
         (307 letters)



>FitnessBrowser__Marino:GFF2762
          Length = 291

 Score =  169 bits (428), Expect = 7e-47
 Identities = 94/301 (31%), Positives = 165/301 (54%), Gaps = 14/301 (4%)

Query: 7   YLQQLVNGLTVGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSYIAFIAITLLAMMGLD 66
           +LQ L  G+T+G+TYALIA+G+T++Y    +INFA GE  MIG          +A + L 
Sbjct: 5   FLQYLFTGITIGATYALIALGFTLIYNASHVINFAQGEFLMIGG---------MATVSLT 55

Query: 67  SVPLMMLAAFAASIIVTSAFGYSIERVAYRPLRGGNRLIPLISAIGMSIFLQNAVMLSQD 126
           ++ + M+ A   ++I+    G +++R A  P +  + +  +I  IG SIF++    +   
Sbjct: 56  AMGVPMILAVVLAVILAGILGVALQRFAIAPAKQADVVTLIIITIGASIFIRGIAQVVWG 115

Query: 127 SKEKAIPTLLPGNFVFGESSMNGVVISYMQILIFVVTFLVMFGLTLFISRSRLGRACRAC 186
            +   +        +     + G V++   + +  +  +++ GL LF +++ +G+A  A 
Sbjct: 116 KEYHVMQNFSTDQPI----EVFGAVLNSQSLWVLGIGAILVVGLVLFFTKTLIGKAILAT 171

Query: 187 AEDLKMTNLLGINSNNIIALTFVIGAALAAVAAVLLGMQYGVINPGIGFLAGIKAFTAAV 246
           + + +   L+GI +  ++ L F++ A L +VA +++       +  IG + G+K F AA 
Sbjct: 172 SMNKEAARLVGIRTQMVLMLAFMVSALLGSVAGIVVA-PITFTSYDIGIILGLKGFVAAA 230

Query: 247 LGGIGSIPGAMLGGLLLGVAEAFGADVFGDQYKDVVAFGLLILVLLFRPTGILGRPEVEK 306
           +GG+GS  GA++GGL LG+ EA  A      YKD VAF +++LVL F P G+ G   VE+
Sbjct: 231 IGGLGSGVGAVVGGLSLGIVEAMAAGYISSDYKDAVAFSMILLVLFFMPRGLFGAKVVER 290

Query: 307 V 307
           V
Sbjct: 291 V 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: 275
Number of extensions: 12
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: 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 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