GapMind for catabolism of small carbon sources

 

Aligments for a candidate for livM in Phaeobacter inhibens BS107

Align ABC transporter membrane-spanning permease-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized)
to candidate GFF3205 PGA1_c32580 high-affinity branched-chain amino acid transport permease protein

Query= TCDB::Q8DQH9
         (318 letters)



>lcl|FitnessBrowser__Phaeo:GFF3205 PGA1_c32580 high-affinity
           branched-chain amino acid transport permease protein
          Length = 358

 Score =  139 bits (350), Expect = 1e-37
 Identities = 99/315 (31%), Positives = 162/315 (51%), Gaps = 34/315 (10%)

Query: 22  ISVLVSVGVLNLFYVQ-ILQQIGINIILAVGLNLIVGFSGQFSLGHAGFMAIGAYAAAII 80
           ++ LV   V+N ++   IL    I  I A+GLN++VG+ GQ SLG  GFMA+GAYA   +
Sbjct: 35  LAFLVVPFVVNDYWANAILLPFLIYSIAAIGLNILVGYCGQVSLGTGGFMAVGAYACYKL 94

Query: 81  GSKSPTYGAFFGAMLVGALLSGAVALLVGIPTLRLKGDYLAVATLGVSEIIRIFIIN--- 137
            +  P    F   +L G  ++  V +  G+P+LR+KG YLAVATL  ++   +++ N   
Sbjct: 95  MTAFPEMSMFIHVLLAGG-ITALVCIGFGLPSLRIKGFYLAVATL-AAQFFLVWLFNRVP 152

Query: 138 -------GGSLTNGAAGILGI----PNFTTWQMVYF---FVVITTIATLNFLRSPIGRST 183
                   G ++     + GI    PN   W    F   F+    +   N  R  +GRS 
Sbjct: 153 WFYNYSASGQISAPERDVFGIIITGPNAPAWATYMFSLIFLAFCALVARNLTRGTVGRSW 212

Query: 184 LSVREDEIAAESVGVNTTKIKIIAFVFGAITASIAGSL-QAGFIGSV-VPKDYTFINSIN 241
           +++R+ +IAAE +GVN  K K+ AF        ++G+L  + ++G+V V + +    S  
Sbjct: 213 MAIRDMDIAAEIIGVNPLKAKLSAFGVSGFFIGVSGALFFSVYLGAVEVGEAFGINKSFL 272

Query: 242 VLIIVVFGGLGSITGAIVSAIVLGILNMLLQ------------DVASVRMIIYALALVLV 289
           VL +V+ GGLGSI G+   A  L +L ++L+             VA ++++I    +V+ 
Sbjct: 273 VLFMVIIGGLGSIFGSFAGAAFLVLLPVVLKVVGVDVLGWPTDIVAHIQLVIVGALIVIF 332

Query: 290 MIFRPGGLLGTWELS 304
           +I  P G+   W ++
Sbjct: 333 LIAEPHGIAQLWRVA 347


Lambda     K      H
   0.327    0.143    0.403 

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: 261
Number of extensions: 18
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: 318
Length of database: 358
Length adjustment: 28
Effective length of query: 290
Effective length of database: 330
Effective search space:    95700
Effective search space used:    95700
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 (21.6 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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