GapMind for catabolism of small carbon sources

 

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

Align HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized)
to candidate H281DRAFT_00655 H281DRAFT_00655 putative spermidine/putrescine transport system ATP-binding protein

Query= TCDB::Q9KKE1
         (275 letters)



>FitnessBrowser__Burk376:H281DRAFT_00655
          Length = 359

 Score =  171 bits (434), Expect = 2e-47
 Identities = 91/237 (38%), Positives = 136/237 (57%), Gaps = 6/237 (2%)

Query: 28  LDKADILSRSGCTVGLNDVSLKIGAGKIFVIMGLSGSGKSTLVRHINRLIEPTSGEVLFD 87
           L+   I  R G  V L    L + AG+   ++G SGSGK+TL++ I+ L+ P++G +  D
Sbjct: 5   LEAIGIAKRYGDAVALEPTDLAVQAGEFLTLLGPSGSGKTTLLQMISGLVAPSAGRIEID 64

Query: 88  GDNILDLGAKALRAFRMRRVSMVFQSFALMPHRTVLQNVVYGQRVRGVSKDDAREIGMKW 147
           G ++  +          R + MVFQS+AL PH +V  NV YG R+R  S+D+ R      
Sbjct: 65  GRDVTHVEPGK------RGIGMVFQSYALFPHMSVWDNVAYGLRMRRKSRDEVRGAVDDA 118

Query: 148 IDTVGLSGYDAKFPHQLSGGMKQRVGLARALAADTDVILMDEAFSALDPLIRGDMQDQLL 207
           +  V ++ Y  +FP +LSGG +QR+ LAR  A    VIL+DE   ALD  +R  MQ ++ 
Sbjct: 119 LAMVRMTEYAKRFPKELSGGQQQRIALARCFAYRPSVILLDEPLGALDKKLREHMQSEIR 178

Query: 208 QLQRNLAKTIVFITHDLDEALRIGSEIAILRDGQVVQVGTPNDILDNPANDYVARFV 264
           +L + L  T V++THD DEAL +   I ++   ++ QVGTP D+ D PA  + A F+
Sbjct: 179 RLHKELGATFVYVTHDQDEALTLSDRICLMNQARIEQVGTPADLYDRPATRFAAGFI 235


Lambda     K      H
   0.323    0.139    0.397 

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: 271
Number of extensions: 11
Number of successful extensions: 2
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: 275
Length of database: 359
Length adjustment: 27
Effective length of query: 248
Effective length of database: 332
Effective search space:    82336
Effective search space used:    82336
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 (21.9 bits)
S2: 48 (23.1 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