GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aapP in Stutzerimonas stutzeri A1501

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 WP_011911265.1 PST_RS00075 ectoine/hydroxyectoine ABC transporter ATP-binding protein EhuA

Query= TCDB::Q52815
         (257 letters)



>NCBI__GCF_000013785.1:WP_011911265.1
          Length = 279

 Score =  224 bits (570), Expect = 2e-63
 Identities = 126/266 (47%), Positives = 166/266 (62%), Gaps = 20/266 (7%)

Query: 2   AEAPAKKLTVSATEVAVEIVNMNKWYGDFHVLRDINLKVMRGERIVIAGPSGSGKSTMIR 61
           A APA+ +        V   ++ K YG+  VL  ++L V  GE++ I GPSGSGKST++R
Sbjct: 18  AAAPAQPM--------VRFASVTKRYGELTVLEGLDLDVQEGEKVAIIGPSGSGKSTLLR 69

Query: 62  CINRLEEHQKGKIVVDGTELTN-----------DLKKIDEVRREVGMVFQHFNLFPHLTI 110
            +  LE    G I VDG  LT+           + + +  VR +VGMVFQ FNLFPH+  
Sbjct: 70  VLMTLEGIDDGLIEVDGEPLTHMPDGHGRLVPANARHLRRVRGKVGMVFQSFNLFPHMNA 129

Query: 111 LENCTLAPIWVRKMPKKQAEEVAMHFLKRVKIPEQANKYPGQLSGGQQQRVAIARSLCMN 170
           L+N   AP+ V  + K++A E A   L  V + ++   +P QLSGGQQQRVAIAR+L M 
Sbjct: 130 LQNVMEAPVQVLGLSKREARERAEELLAMVGLEDKLEHFPAQLSGGQQQRVAIARALAMR 189

Query: 171 PKIMLFDEPTSALDPEMIKEVLDTMVGLAE-EGMTMLCVTHEMGFARQVANRVIFMDQGQ 229
           PK+MLFDE TSALDPE+  EVL  +  L E   +TML VTH+MGFAR+ A+RV F  QG+
Sbjct: 190 PKVMLFDEVTSALDPELCGEVLSVIRRLGEAHNLTMLMVTHQMGFAREFADRVCFFHQGR 249

Query: 230 IVEQNEPAAFFDNPQHERTKLFLSQI 255
           I EQ  P A F+NPQ +RT+ FLS +
Sbjct: 250 IHEQGSPDALFNNPQEDRTREFLSAV 275


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: 209
Number of extensions: 8
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: 257
Length of database: 279
Length adjustment: 25
Effective length of query: 232
Effective length of database: 254
Effective search space:    58928
Effective search space used:    58928
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 Apr 09 2024. 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