GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aapP in Herbaspirillum seropedicae SmR1

Align AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized)
to candidate HSERO_RS05835 HSERO_RS05835 arginine ABC transporter ATP-binding protein

Query= TCDB::Q52815
         (257 letters)



>FitnessBrowser__HerbieS:HSERO_RS05835
          Length = 242

 Score =  254 bits (648), Expect = 2e-72
 Identities = 126/239 (52%), Positives = 167/239 (69%)

Query: 18  VEIVNMNKWYGDFHVLRDINLKVMRGERIVIAGPSGSGKSTMIRCINRLEEHQKGKIVVD 77
           +E+  ++K +G   VL+D++L V +GE + + GPSGSGKST++RCIN LE +++G I++D
Sbjct: 2   IEVKRISKCFGRHEVLKDVSLSVAQGEVVCLIGPSGSGKSTVLRCINGLESYERGDILID 61

Query: 78  GTELTNDLKKIDEVRREVGMVFQHFNLFPHLTILENCTLAPIWVRKMPKKQAEEVAMHFL 137
           G  +  D   I  +R  VGMVFQ FNLFPH T+LEN T  PI+V  + + QA   AM  L
Sbjct: 62  GQRVDRDGPDIHRLRTRVGMVFQRFNLFPHRTVLENVTEGPIYVNGLARAQARSEAMSLL 121

Query: 138 KRVKIPEQANKYPGQLSGGQQQRVAIARSLCMNPKIMLFDEPTSALDPEMIKEVLDTMVG 197
            +V +  + + YP QLSGGQQQRVAIARSL M P+ +LFDEPTSALDPE++ EVL  M  
Sbjct: 122 DKVGLAARCDAYPAQLSGGQQQRVAIARSLAMQPEAILFDEPTSALDPELVGEVLAVMRT 181

Query: 198 LAEEGMTMLCVTHEMGFARQVANRVIFMDQGQIVEQNEPAAFFDNPQHERTKLFLSQIL 256
           LA +GMTM+ VTHEMGFAR+VA+RV F+  G IVE    A     PQH RT+ FL +++
Sbjct: 182 LAADGMTMIVVTHEMGFAREVADRVCFLHSGSIVESGAAAQVLAEPQHARTQDFLRRVI 240


Lambda     K      H
   0.321    0.135    0.394 

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: 204
Number of extensions: 5
Number of successful extensions: 1
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: 257
Length of database: 242
Length adjustment: 24
Effective length of query: 233
Effective length of database: 218
Effective search space:    50794
Effective search space used:    50794
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: 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