GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hutV in Marinobacter adhaerens HP15

Align HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized)
to candidate GFF1015 HP15_994 glycine betaine/carnitine/choline ABC transporter ATP-binding protein

Query= TCDB::Q9KKE1
         (275 letters)



>FitnessBrowser__Marino:GFF1015
          Length = 315

 Score =  163 bits (412), Expect = 5e-45
 Identities = 87/242 (35%), Positives = 150/242 (61%), Gaps = 6/242 (2%)

Query: 28  LDKADILSRSGCTVGLNDVSLKIGAGKIFVIMGLSGSGKSTLVRHINRLIEPTSGEVLFD 87
           ++  ++  R G  V ++ ++L +  G++ V++G SG GKST +R IN+L+  + G++L D
Sbjct: 2   IELKNVTRRFGDAVAVDRINLTVETGEVCVLVGSSGCGKSTTLRMINQLLPHSEGQILVD 61

Query: 88  GDNILDLGAKALRAFRMRRVSMVFQSFALMPHRTVLQNVVYGQRVRGVSKDDAREIGMKW 147
           G+++  +  + LR      +  V Q   L PH TV +N+    ++    ++   E   + 
Sbjct: 62  GNDVTAMNPEQLRL----NMGYVIQGTGLFPHWTVARNIAMVPQLLKWPRERVDERVHEL 117

Query: 148 IDTVGL--SGYDAKFPHQLSGGMKQRVGLARALAADTDVILMDEAFSALDPLIRGDMQDQ 205
           +  + L  + +  K+P QLSGG  QRVG+ARALAA+ +++LMDE F ALD + R ++Q +
Sbjct: 118 LTLLDLDPATHANKYPQQLSGGQAQRVGVARALAANPNILLMDEPFGALDAITRENLQLE 177

Query: 206 LLQLQRNLAKTIVFITHDLDEALRIGSEIAILRDGQVVQVGTPNDILDNPANDYVARFVQ 265
           +L++Q  L KT VF+THD+DEALR+ + IA++  G+++Q  TP +IL  PA+ +V   V 
Sbjct: 178 MLRIQSQLRKTTVFVTHDIDEALRLATRIAVMDQGRIIQHDTPENILRRPASVFVENLVG 237

Query: 266 RR 267
           ++
Sbjct: 238 KQ 239


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: 240
Number of extensions: 12
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: 315
Length adjustment: 26
Effective length of query: 249
Effective length of database: 289
Effective search space:    71961
Effective search space used:    71961
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