GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aglK in Azospirillum brasilense Sp245

Align ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized)
to candidate AZOBR_RS30410 AZOBR_RS30410 ABC transporter ATP-binding protein

Query= reanno::Smeli:SMc03065
         (362 letters)



>FitnessBrowser__azobra:AZOBR_RS30410
          Length = 371

 Score =  247 bits (631), Expect = 3e-70
 Identities = 138/290 (47%), Positives = 180/290 (62%), Gaps = 6/290 (2%)

Query: 3   GLLLKDIRKSYGAVDVIHGIDLDIKEGEFVVFVGPSGCGKSTLLRMIAGLEEITGGDMFI 62
           G+ +  +  SYG+  V+  I LDIK GEF  F+GPSGCGK+TLLR+IAG      G + I
Sbjct: 18  GVRIDGVDLSYGSHRVLKDIHLDIKPGEFFAFLGPSGCGKTTLLRLIAGFNTAQRGAVTI 77

Query: 63  DGERVNDVPPSKRGIAMVFQSYALYPHMTVYDNMAFGMRIARESKEEIDRRVRGAADMLQ 122
            G  ++ +P  KR + MVFQSYAL+PHMTV  N+AFG+   R  + EI+RRV  A D++ 
Sbjct: 78  GGRDISGLPAHKRDVGMVFQSYALWPHMTVRRNVAFGLEERRVPRAEIERRVDAALDLVG 137

Query: 123 LTPYLDRLPKALSGGQRQRVAIGRAICRNPKVFLFDEPLSNLDAALRVATRIEIAKLSER 182
           L    DR P  LSGGQ+QRVA+ R I   PKV L DEPLSNLDA LRV  R E+  L  +
Sbjct: 138 LKHLADRRPSQLSGGQQQRVALARTIVIEPKVLLLDEPLSNLDAKLRVQMRQELLSLQRK 197

Query: 183 MSDTTMIYVTHDQVEAMTLADRIVVLSAGHIEQVGAPLELYERPANLFVARFIGSPAMNV 242
           +  TT I+VTHDQ EA T+ DRI V+  G ++QVG P ELY+ PANLFVA F+G+   NV
Sbjct: 198 LGLTT-IFVTHDQEEANTICDRIAVMEDGIVQQVGTPQELYDHPANLFVAGFLGT--ANV 254

Query: 243 IPATITATGQQTAVSLAGGKSVTLDVPTNASENGKTASFGVRPEDLRVTE 292
           +   + A    TA  + GG  + L    +  E G       RP++L + +
Sbjct: 255 LEGQVRAVDGGTAFVMGGGVPIPL---PHGVEPGAAGKLMFRPQNLFIRQ 301


Lambda     K      H
   0.320    0.137    0.387 

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: 365
Number of extensions: 13
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 362
Length of database: 371
Length adjustment: 30
Effective length of query: 332
Effective length of database: 341
Effective search space:   113212
Effective search space used:   113212
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 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