GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hutV in Dechlorosoma suillum PS

Align HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized)
to candidate Dsui_0258 Dsui_0258 sulfate ABC transporter, ATP-binding protein

Query= TCDB::Q9KKE1
         (275 letters)



>FitnessBrowser__PS:Dsui_0258
          Length = 360

 Score =  158 bits (399), Expect = 2e-43
 Identities = 88/237 (37%), Positives = 139/237 (58%), Gaps = 10/237 (4%)

Query: 32  DILSRSGCTVGLNDVSLKIGAGKIFVIMGLSGSGKSTLVRHINRLIEPTSGEVLFDGDNI 91
           +I  R G  V L+DVSL I  G++  ++G SG GK+TL+R I  +     G+V+F+G   
Sbjct: 7   NIAKRFGNFVALDDVSLSIPTGELVALLGPSGCGKTTLLRIIAGMETADEGQVMFEGSEA 66

Query: 92  LDLGAKALRAFRMRRVSMVFQSFALMPHRTVLQNVVYGQRVRGVSK----DDAREIGMKW 147
             L A      R R+V  VFQ +AL  H  V +NV +G RV+   +     + R+  M  
Sbjct: 67  THLHA------RERQVGFVFQHYALFRHMNVFENVAFGLRVKPRKERPCESEIRKRVMDL 120

Query: 148 IDTVGLSGYDAKFPHQLSGGMKQRVGLARALAADTDVILMDEAFSALDPLIRGDMQDQLL 207
           +  V L     ++P QLSGG +QR+ LARALA +  V+L+DE F ALD  +R +++  L 
Sbjct: 121 LSLVQLDWLADRYPTQLSGGQRQRIALARALAVEPKVLLLDEPFGALDTKVRKELRRWLR 180

Query: 208 QLQRNLAKTIVFITHDLDEALRIGSEIAILRDGQVVQVGTPNDILDNPANDYVARFV 264
           +L   +  + VF+THD +EAL +   + ++  G++ QVG+P+++  NPA+ +V +F+
Sbjct: 181 RLHDEMHISSVFVTHDQEEALEVADRVVVMNKGRIEQVGSPDEVYSNPASPFVYQFL 237


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: 245
Number of extensions: 11
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: 275
Length of database: 360
Length adjustment: 27
Effective length of query: 248
Effective length of database: 333
Effective search space:    82584
Effective search space used:    82584
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