GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aapP in Phaeobacter inhibens BS107

Align ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component (characterized)
to candidate GFF1143 PGA1_c11580 octopine permease ATP-binding protein P

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



>FitnessBrowser__Phaeo:GFF1143
          Length = 259

 Score =  211 bits (537), Expect = 1e-59
 Identities = 109/257 (42%), Positives = 161/257 (62%), Gaps = 10/257 (3%)

Query: 12  VSTTDVAIEITNMNKWYGDFHVLRDINLRVMRGERIVVAGPSGSGKSTMIRCINRLEEHQ 71
           ++ T   +EI  ++K YG+  V++ +++   RG+ + + G SGSGKST++RC N LE+ Q
Sbjct: 1   MTDTTPVLEIRGLHKSYGELEVIKGVDITAHRGDVVSLIGSSGSGKSTLLRCCNLLEDSQ 60

Query: 72  KGKIVVDGIELT----------NDLKKIDEVRREVGMVFQHFNLFPHLTILENCTLAPIW 121
           +G I+  G  +           +D K++  +R  + MVFQ FNL+ H+TIL+N   AP+ 
Sbjct: 61  EGDILFKGEPINWSGTGLARRPSDAKQVLRIRTNLSMVFQQFNLWAHMTILQNVMEAPLT 120

Query: 122 VRKMPKKEAEQVAMHFLERVKIPEQALKYPGQLSGGQQQRVAIARSLCMRPKILLFDEPT 181
           V    + E E  A  +L +V I ++   YP QLSGGQQQR AIAR+LCM P+ LLFDEPT
Sbjct: 121 VLGRDRAEVEDAARKYLTKVGIGDKCDAYPAQLSGGQQQRAAIARALCMEPEALLFDEPT 180

Query: 182 SALDPEMVKEVLDTMVGLAEEGMTMICVTHEMGFARQVANRVIFMDQGQIVEQNSPAEFF 241
           SALDPE+ +EV+  +  LA EG TMI VTH+M  A  V++ ++F+ +G I E+  P E F
Sbjct: 181 SALDPELEQEVVKVIKDLAAEGRTMIIVTHDMNMAADVSSHIVFLHKGLIEEEGCPDEVF 240

Query: 242 DNPQHERTKLFLSQILH 258
            + + ER + FL+   H
Sbjct: 241 GSTRSERLRGFLASTRH 257


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: 162
Number of extensions: 5
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: 259
Length adjustment: 24
Effective length of query: 234
Effective length of database: 235
Effective search space:    54990
Effective search space used:    54990
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