GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livM in Marinobacter adhaerens HP15

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 GFF3114 HP15_3057 leucine/isoleucine/valine transporter permease subunit

Query= TCDB::P21628
         (417 letters)



>FitnessBrowser__Marino:GFF3114
          Length = 423

 Score =  507 bits (1305), Expect = e-148
 Identities = 252/419 (60%), Positives = 324/419 (77%), Gaps = 5/419 (1%)

Query: 2   SQSLKRALFSALLVILVSYPILGLKLRTVGIKLEVLGADAQTLWTIAAAALAMFVWQLFR 61
           + + + ALF A + +++SYPI+G  L   GI + + GADA T+  +  AA+ +F++Q+FR
Sbjct: 3   ANNFRHALFCAFITLIISYPIIGFNLEAQGINVTLTGADASTIVMVLFAAVIVFLFQMFR 62

Query: 62  DRIPLKLGRGVGYKVNGSGLKNFLS--LPSTQRWAVLALVVVAFVWPFFASRGAVDIATL 119
           ++I   L + + + +  S  +          + W +  +VV+A  WPFF SRGAVD+ATL
Sbjct: 63  EQIMGGL-KSIPHPLPQSNKEPMAENRRAKIESWVLTGIVVLALFWPFFVSRGAVDLATL 121

Query: 120 ILIYVMLGIGLNIVVGLAGLLDLGYVGFYAVGAYTYALLAEYAGFGFWTALPIAGMMAAL 179
           +LIY+ML +GLN+VVGLAGLLDLGYV FYAVGAYT+ALL++Y G  FW ALPI  ++AAL
Sbjct: 122 VLIYIMLALGLNVVVGLAGLLDLGYVAFYAVGAYTFALLSQYTGISFWLALPIGALLAAL 181

Query: 180 FGFLLGFPVLRLRGDYLAIVTLGFGEIIRILLRNMTEITGGPNGIGSIPKPTLFGLTFER 239
           FG +LGFPVLRLRGDYLAIVTLGFGEIIRILL N T +TGGPNGIG IP PTLFG+ F R
Sbjct: 182 FGLVLGFPVLRLRGDYLAIVTLGFGEIIRILLNNWTTLTGGPNGIGGIPDPTLFGMEFGR 241

Query: 240 RA-PEGMQTFHEFFGIAYNTNYKVILLYVVALLLVLLALFVINRLMRMPIGRAWEALRED 298
           R   EG  +FHE FGIAY+  +KVI LY++AL+L +    VI R MRMP+GRAWEALRED
Sbjct: 242 RVKEEGNTSFHETFGIAYSGEHKVIFLYLIALVLAVFTALVIRRFMRMPVGRAWEALRED 301

Query: 299 EVACRALGLNPTIVKLSAFTIGASFAGFAGSFFAARQGLVTPESFTFIESAMILAIVVLG 358
           E+A R+LGL+ T VKLSAFTIGA FAGFAG+ FA++QG ++PESF F+ESA+ILAIVVLG
Sbjct: 302 EIAARSLGLSRTAVKLSAFTIGAFFAGFAGTVFASKQGFISPESFVFLESAIILAIVVLG 361

Query: 359 GMGSQLGVILAAVVMVLLQEM-RGFNEYRMLIFGLTMIVMMIWRPQGLLPMQRPHLELK 416
           GMGSQ+GV+LAA+ + +L E+ R F+EYRMLIFG  M++MM+WRPQGL+PM+R H+ELK
Sbjct: 362 GMGSQIGVVLAAIAVTILPELAREFSEYRMLIFGAAMVLMMVWRPQGLMPMRRIHIELK 420


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: 589
Number of extensions: 30
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: 423
Length adjustment: 32
Effective length of query: 385
Effective length of database: 391
Effective search space:   150535
Effective search space used:   150535
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