GapMind for catabolism of small carbon sources

 

Aligments for a candidate for natE in Pseudomonas stutzeri RCH2

Align NatE, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized)
to candidate GFF1275 Psest_1308 ABC-type branched-chain amino acid transport systems, ATPase component

Query= TCDB::Q8YT15
         (247 letters)



>lcl|FitnessBrowser__psRCH2:GFF1275 Psest_1308 ABC-type
           branched-chain amino acid transport systems, ATPase
           component
          Length = 233

 Score =  223 bits (567), Expect = 3e-63
 Identities = 113/233 (48%), Positives = 160/233 (68%), Gaps = 2/233 (0%)

Query: 11  LLEVENVHAGYIKDVDILQGVNFRVESGELVTVIGPNGAGKSTLAKTIFGLLTPHTGKIT 70
           +L  ENV   Y K +  L  +N +VE GE+VT+IG NGAGKSTL  T+ G     +G I 
Sbjct: 1   MLTFENVSTFYGK-IQALHDINVQVEQGEIVTLIGANGAGKSTLLMTLCGSPQAASGSIR 59

Query: 71  FKGKNIAGLKSNQIVRLGMCYVPQIANVFPSLSVEENLEMGAFIRNDS-LQPLKDKIFAM 129
           F+G+ + G ++  I+R  +  VP+   +F  L+VEENL MG F    +  Q   DK+  +
Sbjct: 60  FQGEELVGRQTCDIMRKAIAVVPEGRRIFARLTVEENLSMGGFFTGKTDFQEQLDKVLGL 119

Query: 130 FPRLSDRRRQRAGTLSGGERQMLAMGKALMLEPSLLVLDEPSAALSPILVTQVFEQVKQI 189
           FPRL +R +QR GT+SGGE+QMLA+ +ALM +P LL+LDEPS  L+PI++ Q+FE ++Q+
Sbjct: 120 FPRLKERYQQRGGTMSGGEQQMLAIARALMSKPKLLLLDEPSLGLAPIIIQQIFEIIEQL 179

Query: 190 NQEGTAIILVEQNARKALEMADRGYVLESGRDAISGPGQELLTDPKVAELYLG 242
            ++G  + LVEQNA +AL++ADRGYVLE+G   + G G++LLTDPKV + YLG
Sbjct: 180 REDGVTVFLVEQNANQALKLADRGYVLENGHIVMQGSGEDLLTDPKVRDAYLG 232


Lambda     K      H
   0.317    0.136    0.377 

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: 193
Number of extensions: 4
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: 247
Length of database: 233
Length adjustment: 23
Effective length of query: 224
Effective length of database: 210
Effective search space:    47040
Effective search space used:    47040
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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