GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SMc02869 in Paraburkholderia bryophila 376MFSha3.1

Align N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized)
to candidate H281DRAFT_05701 H281DRAFT_05701 glycerol 3-phosphate ABC transporter ATP-binding protein

Query= reanno::Smeli:SMc02869
         (352 letters)



>FitnessBrowser__Burk376:H281DRAFT_05701
          Length = 362

 Score =  311 bits (797), Expect = 2e-89
 Identities = 179/360 (49%), Positives = 225/360 (62%), Gaps = 31/360 (8%)

Query: 17  VGSLQLKTIRKAF-GSHEVLKGIDLDVKDGEFVIFVGPSGCGKSTLLRTIAGLEDATSGS 75
           + +L L+ ++K + G   VL GID+DV DGEFV+ VGPSGCGKSTLLR +AGLE  + G+
Sbjct: 1   MAALTLQGVKKTYDGKQFVLHGIDVDVNDGEFVVMVGPSGCGKSTLLRMVAGLERISEGT 60

Query: 76  VQIDGVEVGHVAPAKRGIAMVFQSYALYPHLTVKDNMGLGLKQAGVPKAEIEEKVAKAAG 135
           + I G  V  + P  R IAMVFQ+YALYPH++V +NMG  LK AGV +A+I ++V  AA 
Sbjct: 61  ISIAGKVVNELEPKDRNIAMVFQNYALYPHMSVAENMGYALKIAGVDRAQIAQRVNAAAQ 120

Query: 136 MLSLEPYLARRPAELSGGQRQRVAIGRAIVREPKLFLFDEPLSNLDAALRVNTRLEIARL 195
           +L LEP L R+P ELSGGQRQRVA+GRAIVREP +FLFDEPLSNLDA LRV  RLEI RL
Sbjct: 121 ILELEPLLQRKPRELSGGQRQRVAMGRAIVREPAVFLFDEPLSNLDARLRVQMRLEIQRL 180

Query: 196 HRSLKATMIYVTHDQVEAMTLADKIVVLNAGRIEQVGSPMELYNRPANLFVAGFIGSPQM 255
           H  L  T +YVTHDQ+EAMTLA +++V+N G  EQ+G+P E+Y RPA +FVAGFIGSP M
Sbjct: 181 HARLATTSLYVTHDQIEAMTLAQRVIVMNKGHAEQIGAPTEVYERPATVFVAGFIGSPGM 240

Query: 256 NFIEAAKLGDGE-----------------------AK----TIGIRPEHIGLSRESGDWK 288
           N +E     DG                        AK    T+GIRPEH+   +      
Sbjct: 241 NLLEGRVSDDGSTFDVAGNGPQLPLAGVASIGREVAKGREWTLGIRPEHMSPGQADAPHT 300

Query: 289 GKVI-HVEHLGADTIIYIESETVGLLTVRLFGEHRYATDDIVHATPVIGSMHRFD-ADGR 346
              +   E LGAD + +        +T RL   HR A  + +        +H FD A GR
Sbjct: 301 TLTVDSCELLGADNLAHGRWGKHD-VTARLPHAHRPAAGEALQVALPARHLHFFDPASGR 359


Lambda     K      H
   0.320    0.137    0.393 

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: 358
Number of extensions: 12
Number of successful extensions: 2
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: 352
Length of database: 362
Length adjustment: 29
Effective length of query: 323
Effective length of database: 333
Effective search space:   107559
Effective search space used:   107559
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