GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Phaeo:GFF3205
          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 (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