GapMind for catabolism of small carbon sources

 

Aligments for a candidate for peb1C in Azospirillum brasilense Sp245

Align PEB1C, component of Uptake system for glutamate and aspartate (characterized)
to candidate AZOBR_RS23525 AZOBR_RS23525 ABC transporter ATP-binding protein

Query= TCDB::A3ZI83
         (242 letters)



>lcl|FitnessBrowser__azobra:AZOBR_RS23525 AZOBR_RS23525 ABC
           transporter ATP-binding protein
          Length = 269

 Score =  233 bits (595), Expect = 2e-66
 Identities = 123/242 (50%), Positives = 164/242 (67%), Gaps = 7/242 (2%)

Query: 1   MIELKNVNKYYGTHHVLKNINLSVKEGEKLVIIGPSGSGKSTTIRCMNGLEEVSSGEVVV 60
           +IE++NV K +G+  VLK+++L+V      V+IGPSGSGKST +RC N LE    GE+ +
Sbjct: 1   VIEIRNVYKSFGSTEVLKDVSLTVPPSRTTVVIGPSGSGKSTLLRCCNCLETADRGEIRI 60

Query: 61  NNLVLNHKNK------IEICRKYCAMVFQHFNLYPHMTVLQNLTLAPMKLQKKSKKEAEE 114
           N+  +    K      +   R    MVFQ FNL+PHMT ++N+  AP+ ++  +K EA E
Sbjct: 61  NHRTIIADGKPLPDKELNALRAETGMVFQSFNLFPHMTTVENVMRAPVVVRGMAKAEARE 120

Query: 115 TAFKYLKVVGLLDKANVYPATLSGGQQQRVAIARSLCTKKPYILFDEPTSALDPETIQEV 174
            A + L+ VGL DKA+VYP+TLSGGQ+QR AIAR+L  K   +LFDEPTSALDPE + EV
Sbjct: 121 LAMELLRKVGLGDKADVYPSTLSGGQKQRAAIARALAMKPKVMLFDEPTSALDPELVGEV 180

Query: 175 LDVMKEISHQSNTTMVVVTHEMGFAKEVADRIIFMEDGAIVEENIPSEFFSNPKTERARL 234
           L VMK ++ +   TM+VVTHEMGFA+EVAD ++ M DG IVE   P + F+NP  ER R 
Sbjct: 181 LQVMKTLA-EEGMTMMVVTHEMGFAREVADTVVVMADGRIVESGSPEQIFTNPTQERTRG 239

Query: 235 FL 236
           FL
Sbjct: 240 FL 241


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: 156
Number of extensions: 7
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: 269
Length adjustment: 24
Effective length of query: 218
Effective length of database: 245
Effective search space:    53410
Effective search space used:    53410
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 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