GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livF in Phaeobacter inhibens BS107

Align High-affinity branched-chain amino acid transport ATP-binding protein (characterized, see rationale)
to candidate GFF250 PGA1_c02620 high-affinity branched-chain amino acid transport ATP-binding protein LivF

Query= uniprot:A0A159ZWL6
         (233 letters)



>FitnessBrowser__Phaeo:GFF250
          Length = 257

 Score =  225 bits (573), Expect = 7e-64
 Identities = 113/234 (48%), Positives = 162/234 (69%), Gaps = 2/234 (0%)

Query: 1   MLQFENVSTFYGKIQALHSVNVEVRQGEIVTLIGANGAGKSTLLMTLCGSPQAHSGSIRY 60
           +L   N+ +FYG I A+  V++ V+ G+IVT++GANGAGKSTLL T+ G      GS+ +
Sbjct: 5   LLDIRNLESFYGPIMAIRGVSLSVQAGQIVTVLGANGAGKSTLLKTISGIMDPEKGSVSF 64

Query: 61  MGEELVGQDSSHIMRKSIAVVPEGRRVFARLTVEENLAMGGFF-TDKGDYQEQMDKVLHL 119
            GEE+ G++   I+R+ I  VPEGR VF  L+VEENL +G +   D+ + +     V   
Sbjct: 65  NGEEIQGEEPHRIVRRGIVHVPEGREVFPLLSVEENLTLGAYTRRDQAEIERDRQMVFDY 124

Query: 120 FPRLKERFTQRGGTMSGGEQQMLAIGRALMSKPKLLLLDEPSLGLAPIIIQQIFDIIEQL 179
           FP L ER  Q  GT+SGG+QQMLAIGR LM +P+++LLDEPSLGL+P+++Q+IF I+++L
Sbjct: 125 FPILAERRHQEAGTLSGGQQQMLAIGRGLMLRPRIMLLDEPSLGLSPLLVQEIFGILKRL 184

Query: 180 RKD-GVTVFLVEQNANQALKIADRAYVLENGRVVMQGTGEALLTDPKVREAYLG 232
            +D GVT+ LVEQNA  AL++A   YV+E GR+VM G+ + L+    ++  YLG
Sbjct: 185 NRDEGVTMMLVEQNARIALELAHVGYVMEIGRIVMDGSADRLMESEDIKSFYLG 238


Lambda     K      H
   0.320    0.137    0.381 

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: 157
Number of extensions: 5
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: 233
Length of database: 257
Length adjustment: 24
Effective length of query: 209
Effective length of database: 233
Effective search space:    48697
Effective search space used:    48697
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 46 (22.3 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