GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livF in Dechlorosoma suillum PS

Align High-affinity branched-chain amino acid transport ATP-binding protein (characterized, see rationale)
to candidate Dsui_1113 Dsui_1113 ABC-type branched-chain amino acid transport systems, ATPase component

Query= uniprot:A0A159ZWL6
         (233 letters)



>FitnessBrowser__PS:Dsui_1113
          Length = 278

 Score =  189 bits (479), Expect = 6e-53
 Identities = 103/240 (42%), Positives = 150/240 (62%), Gaps = 9/240 (3%)

Query: 2   LQFENVSTFYGK-IQALHSVNVEVRQGEIVTLIGANGAGKSTLLMTLCGSPQAH-----S 55
           L   N+   Y   I  L  V++ V +G+IV L+GANGAGKST L  +     A       
Sbjct: 16  LSINNIEVIYDHVILVLKGVSLTVPKGKIVALLGANGAGKSTTLKAISNLLHAERGDVTK 75

Query: 56  GSIRYMGEELVGQDSSHIMRKSIAVVPEGRRVFARLTVEENLAMGGFF--TDKGDYQEQM 113
           GS+ + G  +     + ++++ +  V EGR  FA L++EENL  G +     + + ++ +
Sbjct: 76  GSVEFKGTRVDQLTPNELVKRGVIQVMEGRHCFAHLSIEENLLTGAYTRGNSRAELKQNL 135

Query: 114 DKVLHLFPRLKERFTQRGGTMSGGEQQMLAIGRALMSKPKLLLLDEPSLGLAPIIIQQIF 173
           + V H FPRLK R T + G  SGGEQQM AIGRALM+KP+++LLDEPS+GLAP I+++IF
Sbjct: 136 EMVYHYFPRLKTRRTSQAGYTSGGEQQMCAIGRALMAKPEMILLDEPSMGLAPQIVEEIF 195

Query: 174 DIIEQLR-KDGVTVFLVEQNANQALKIADRAYVLENGRVVMQGTGEALLTDPKVREAYLG 232
           +I++ L  ++ V+  L EQN   AL+ AD  Y+LENGRVVM+G  + L ++  V+E YLG
Sbjct: 196 EIVKDLNSRENVSFLLAEQNTMVALRYADLGYILENGRVVMEGDAKELASNEDVKEFYLG 255


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: 165
Number of extensions: 8
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: 233
Length of database: 278
Length adjustment: 24
Effective length of query: 209
Effective length of database: 254
Effective search space:    53086
Effective search space used:    53086
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: 47 (22.7 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