GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hutX in Phaeobacter inhibens BS107

Align HutX aka HISX, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized)
to candidate GFF2248 PGA1_c22800 glycine betaine-binding protein

Query= TCDB::Q9KKE3
         (346 letters)



>FitnessBrowser__Phaeo:GFF2248
          Length = 323

 Score =  151 bits (382), Expect = 2e-41
 Identities = 100/330 (30%), Positives = 162/330 (49%), Gaps = 24/330 (7%)

Query: 20  AASASGANASYCGDGKTVTFAGIDWESGAFITEVMKTILSKGYDCQVDSIP-GNSVTLEQ 78
           A +AS A A  CG+   V+    DW S   +T V K ++ +GY C V ++P  ++  L  
Sbjct: 15  AITASAAQADDCGE---VSIMQGDWGSAQIVTAVAKFLMEEGYGCDVTAMPLSSNPALAS 71

Query: 79  ATANNDVQIFAEEWLGRSDVWNKAVEEKKVIAVGKTFV-GASEGWFVPDYVVHGDPARNI 137
            +   +  I  E W   +  +   V+   +I V +    G  EG+FVP+Y+V        
Sbjct: 72  VSETGEPDILTEIWTNGAPAYQGLVDSGAIIPVTEVLSDGGVEGFFVPNYLVE------- 124

Query: 138 EAKAPDLKSVSQLTDPKIAEIFADPEEPSKGRFLNCPSGWTCEGVSTAKLEAYKLGETYV 197
             + P+L ++  +         A+PE     RF NCP GWTC  VST  ++A  L +  +
Sbjct: 125 --EHPELATIEGIA--------ANPELVGN-RFHNCPEGWTCLNVSTNLMKAGGLIDAGI 173

Query: 198 -NFRPGTGTALDAAITSAYLQGEPIFFYYWSPTAILGKFKLIQLEEPAYNEACWKELSSA 256
            NF  G+G  L A+I +AY   EP F +YW+PT++LGK+ +  ++   ++        +A
Sbjct: 174 ENFVHGSGETLAASIAAAYENKEPWFGFYWAPTSVLGKYPMTLVDMGPHDPEKHACNITA 233

Query: 257 NGKRDEGCAFPSVDVAYGVNSTFASEAPEIVEILEKATFPLDEVNASLAYMADNKVDATA 316
                   AFP  +V   ++  F +E  EI E++   +F   ++  +LA++ DN      
Sbjct: 234 ECDTPAMSAFPRSEVVTVLSKEFMAENAEISELMTNLSFTNAQMGETLAWVEDNNASYDE 293

Query: 317 AAAEFLKTKGDIWSKWVSDEARGKIEAGLK 346
            A  FL T  D+W  W++D AR K+ A L+
Sbjct: 294 GAVHFLTTYKDVWGAWLNDAARDKLSALLQ 323


Lambda     K      H
   0.314    0.130    0.391 

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: 285
Number of extensions: 12
Number of successful extensions: 5
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: 346
Length of database: 323
Length adjustment: 28
Effective length of query: 318
Effective length of database: 295
Effective search space:    93810
Effective search space used:    93810
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 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