GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glpT in Cronobacter universalis NCTC 9529

Align GlpT, component of Glycerol uptake porter, GlpSTPQV (characterized)
to candidate WP_038857067.1 AFK65_RS10835 ABC transporter ATP-binding protein

Query= TCDB::G3LHY9
         (356 letters)



>NCBI__GCF_001277175.1:WP_038857067.1
          Length = 360

 Score =  213 bits (542), Expect = 6e-60
 Identities = 127/347 (36%), Positives = 197/347 (56%), Gaps = 19/347 (5%)

Query: 1   MARITLDHIRHAYGANPKSDKDYSLKEVDHEWNDGGAYALLGPSGCGKTTLLNIISGLLQ 60
           MA+++L HI+  Y       KD++L+  D E+        +GPSGCGK+T L +I+GL  
Sbjct: 1   MAQLSLQHIQKIYDNQVHVVKDFNLEIADKEF-----IVFVGPSGCGKSTTLRMIAGLEA 55

Query: 61  PSHGRILFDGKDVTNLSTQSRNIAQVFQFPVIYDTMTVYDNLAFPLRNRGVAEADVDRRV 120
            S G +L DG  + ++  ++RNIA VFQ   +Y  MTVYDN+AF L+ + VA A ++ RV
Sbjct: 56  ISGGDLLIDGVRMNDVPAKARNIAMVFQNYALYPHMTVYDNMAFGLKMQKVAPAIIEERV 115

Query: 121 RDILEMIDLASWARRKAQGLTADQKQKISLGRGLVRNDVNAILFDEPLTVIDPHMKWVLR 180
               +++ L  + +RK   L+  Q+Q+++LGR +VR +    L DEPL+ +D  ++  +R
Sbjct: 116 AWAAQILGLKEYLKRKPGALSGGQRQRVALGRAIVR-EAGVFLMDEPLSNLDAKLRVQMR 174

Query: 181 SQLKRLHKQFGFTMVYVTHDQTEALTFAEKVVVMYDGQIVQIGTPAELFERPSHTFVGYF 240
           +++ +LH++   TM+YVTHDQTEA+T A ++V+M DG + Q+G P E++  P++ FV  F
Sbjct: 175 AEISKLHQKLNTTMIYVTHDQTEAMTMATRIVIMKDGIVQQVGAPKEVYNHPANMFVAGF 234

Query: 241 IGSPGMNFMPARIEGSTVKVGDETLTLEYAP------KTSGTAK--TELGIRPEFI---R 289
           IGSP MNF+   I+G       ETL L            SG  +    LGIRPE I    
Sbjct: 235 IGSPAMNFIRGAIDGEYFVT--ETLKLPLPVNKLARLNDSGYQRKAVVLGIRPEDIFPGA 292

Query: 290 LGREGMPITISKVEDIGRQKIVRARFADQPIAIVVPEDADIPADARV 336
            G + +   I+  E  G + ++ A      + +    D D  AD R+
Sbjct: 293 TGDDAIEAKITVAELTGAEFMLYATVGGHEMVVRAGADKDYQADQRI 339


Lambda     K      H
   0.321    0.137    0.405 

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: 319
Number of extensions: 15
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: 356
Length of database: 360
Length adjustment: 29
Effective length of query: 327
Effective length of database: 331
Effective search space:   108237
Effective search space used:   108237
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 (21.8 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Sep 24 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