GapMind for catabolism of small carbon sources

 

Alignments for a candidate for peb1C in Paraburkholderia bryophila 376MFSha3.1

Align PEB1C, component of Uptake system for glutamate and aspartate (characterized)
to candidate H281DRAFT_03348 H281DRAFT_03348 amino acid ABC transporter ATP-binding protein, PAAT family

Query= TCDB::A3ZI83
         (242 letters)



>FitnessBrowser__Burk376:H281DRAFT_03348
          Length = 258

 Score =  222 bits (566), Expect = 5e-63
 Identities = 118/246 (47%), Positives = 161/246 (65%), Gaps = 7/246 (2%)

Query: 1   MIELKNVNKYYGTHHVLKNINLSVKEGEKLVIIGPSGSGKSTTIRCMNGLEEVSSGEV-- 58
           ++ ++ + K +G+H VL  I+  +   + +V+IGPSGSGKST +RC NGLE+   G +  
Sbjct: 11  IVSIRGLTKSFGSHTVLNGIDFDIHPQQVVVVIGPSGSGKSTFLRCCNGLEQAERGTIDI 70

Query: 59  ----VVNNLVLNHKNKIEICRKYCAMVFQHFNLYPHMTVLQNLTLAPMKLQKKSKKEAEE 114
               +V+   +  +  +   R    MVFQ FNL+PH++VL N+T+ P  L+  SK +AE 
Sbjct: 71  CGHRLVDQGAMLKERSLNALRTEVGMVFQSFNLFPHLSVLHNITVGPRMLRGASKAQAEA 130

Query: 115 TAFKYLKVVGLLDKANVYPATLSGGQQQRVAIARSLCTKKPYILFDEPTSALDPETIQEV 174
            A   L+ VGL  KA+V PA+LSGGQ+QRVAIAR+L  +   +LFDEPTSALDPE + EV
Sbjct: 131 AAIALLEKVGLAHKADVMPASLSGGQKQRVAIARALAMQPRVMLFDEPTSALDPELVGEV 190

Query: 175 LDVMKEISHQSNTTMVVVTHEMGFAKEVADRIIFMEDGAIVEENIPSEFFSNPKTERARL 234
           L VMK ++ +   TMVVVTHEMGFAKEVAD ++ M+ G IVE   P+E FS P   R R 
Sbjct: 191 LQVMKLLASE-GMTMVVVTHEMGFAKEVADVVVVMDGGVIVEAGPPAEIFSAPSQPRTRA 249

Query: 235 FLGKIL 240
           FL  +L
Sbjct: 250 FLQAVL 255


Lambda     K      H
   0.317    0.133    0.372 

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: 147
Number of extensions: 6
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: 242
Length of database: 258
Length adjustment: 24
Effective length of query: 218
Effective length of database: 234
Effective search space:    51012
Effective search space used:    51012
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 (21.7 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