GapMind for catabolism of small carbon sources

 

Alignments for a candidate for peb1C in Phaeobacter inhibens BS107

Align PEB1C, component of Uptake system for glutamate and aspartate (characterized)
to candidate GFF3831 PGA1_262p02350 histidine transport ATP-binding protein HisP

Query= TCDB::A3ZI83
         (242 letters)



>FitnessBrowser__Phaeo:GFF3831
          Length = 281

 Score =  208 bits (529), Expect = 1e-58
 Identities = 112/246 (45%), Positives = 164/246 (66%), Gaps = 9/246 (3%)

Query: 2   IELKNVNKYYGTHHVLKNINLSVKEGEKLVIIGPSGSGKSTTIRCMNGLEEVSSGEVVVN 61
           I + +++K +G+  VLK ++L+ K+G+ + IIG SGSGKST +RC+N LE  +SGE+V+ 
Sbjct: 36  IRVCDLHKSFGSLEVLKGVSLTAKQGDVVAIIGGSGSGKSTMLRCINFLETPNSGEIVIA 95

Query: 62  NLVLN--------HKNKIEICRKYCAMVFQHFNLYPHMTVLQNLTLAPMKLQKKSKKEAE 113
              +          + +IE  R   AMVFQ FNL+ H T+L+N+   P+ + K  + EA 
Sbjct: 96  GETVAMRQDGSPADRRQIERIRTRLAMVFQQFNLWTHRTLLENVIEVPVHVLKVPRSEAI 155

Query: 114 ETAFKYLKVVGLLDKANVYPATLSGGQQQRVAIARSLCTKKPYILFDEPTSALDPETIQE 173
             A + L  VGL DKA+ +PA LSGGQQQR AIAR+L      +LFDEPTSALDPE + E
Sbjct: 156 HRAHELLARVGLGDKADAFPAFLSGGQQQRAAIARALAVDPNVMLFDEPTSALDPELVGE 215

Query: 174 VLDVMKEISHQSNTTMVVVTHEMGFAKEVADRIIFMEDGAIVEENIPSEFFSNPKTERAR 233
           VL V+++++ +   TM++VTHEM FA+EVA+ ++++ +G I E+  PSE F NPK+ER +
Sbjct: 216 VLTVIRDLAAEGR-TMLLVTHEMKFAREVANHVVYLFEGRIEEQGPPSEVFGNPKSERLK 274

Query: 234 LFLGKI 239
            FL  +
Sbjct: 275 QFLSSV 280


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: 143
Number of extensions: 4
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: 281
Length adjustment: 25
Effective length of query: 217
Effective length of database: 256
Effective search space:    55552
Effective search space used:    55552
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: 47 (22.7 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