GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aapP in Paraburkholderia bryophila 376MFSha3.1

Align ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component (characterized)
to candidate H281DRAFT_05873 H281DRAFT_05873 amino acid ABC transporter ATP-binding protein, PAAT family

Query= reanno::Smeli:SMc02121
         (258 letters)



>FitnessBrowser__Burk376:H281DRAFT_05873
          Length = 250

 Score =  241 bits (616), Expect = 8e-69
 Identities = 129/239 (53%), Positives = 168/239 (70%), Gaps = 1/239 (0%)

Query: 19  IEITNMNKWYGDFHVLRDINLRVMRGERIVVAGPSGSGKSTMIRCINRLEEHQKGKIVVD 78
           I ++ ++K +G   VL DINL V  GE +V+ G SGSGKST++R +  LE    G++ V+
Sbjct: 11  ISLSGVSKSFGATRVLNDINLDVRAGEVLVLIGASGSGKSTVLRIMAGLETTDSGEVWVN 70

Query: 79  GIELTNDLKKIDEVRREVGMVFQHFNLFPHLTILENCTLAPIWVRKMPKKEAEQVAMHFL 138
            + L +D K+  E+R  VGMVFQ FNLFPH T L N TLA I  R M   +A + AM  L
Sbjct: 71  EVPL-HDPKRAREIRGHVGMVFQQFNLFPHKTALGNVTLALIKARGMSPADARKRAMDSL 129

Query: 139 ERVKIPEQALKYPGQLSGGQQQRVAIARSLCMRPKILLFDEPTSALDPEMVKEVLDTMVG 198
           +RV + ++A  YP QLSGGQQQRVAIAR+L + P I+ FDE TSALDPE+V EV + M G
Sbjct: 130 DRVGLADRASHYPSQLSGGQQQRVAIARALAVEPGIMFFDEATSALDPELVGEVTEVMRG 189

Query: 199 LAEEGMTMICVTHEMGFARQVANRVIFMDQGQIVEQNSPAEFFDNPQHERTKLFLSQIL 257
           LA +GMTM+ VTHEMGFAR+ A+RV+FMD+G I EQ  P + F NP +ERT+ FLS++L
Sbjct: 190 LARDGMTMVVVTHEMGFARKTADRVLFMDKGVIAEQGDPEQIFVNPSNERTRQFLSRVL 248


Lambda     K      H
   0.322    0.136    0.397 

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: 189
Number of extensions: 6
Number of successful extensions: 2
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: 258
Length of database: 250
Length adjustment: 24
Effective length of query: 234
Effective length of database: 226
Effective search space:    52884
Effective search space used:    52884
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 (21.9 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