GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gtsC in Pseudovibrio axinellae Ad2

Align Sugar transport system permease protein aka TT_C0326, component of The glucose/mannose porter TTC0326-8 plus MalK1 (ABC protein, shared with 3.A.1.1.25) (characterized)
to candidate WP_068010603.1 PsAD2_RS21750 carbohydrate ABC transporter permease

Query= TCDB::Q72KX4
         (268 letters)



>NCBI__GCF_001623255.1:WP_068010603.1
          Length = 280

 Score =  137 bits (346), Expect = 2e-37
 Identities = 78/270 (28%), Positives = 142/270 (52%), Gaps = 5/270 (1%)

Query: 3   RALLYGFLLLMAGFFLLPVYLVVLTALKEPARITLETVWQWPHPPYWESFRTAWEA--FR 60
           +  LY  + +  GF LLP + + +T+L+    +       W     + ++   WE     
Sbjct: 10  KVFLYICVAIFLGFILLPFFEMFMTSLRPLEHLFRSPYQFWSDDFSFRAYAQMWETVPML 69

Query: 61  PKF-QNSVVLAVSATLLSALVGSLNGYVLAKWPFRGSGLLFALILFGMFIPYQSILIPLF 119
           P++  NS+ +++S T L+ L      Y  A++ F+G  +   + L         +LIPL+
Sbjct: 70  PRYIANSMFISLSVTALALLFIIPAAYAYARFDFKGKSISLGIFLAVNMFSGAVLLIPLY 129

Query: 120 QFMKSIGLYGSLFGLVLVHVIYGIPIVTLIFRNYYSEIPDELVEAARIDGAGFFGIFRHV 179
           + +++ GL  + F +++    + +P+   + ++Y  +IP EL EAA +DGA      R V
Sbjct: 130 KLLRNYGLLNTYFAMIVPGAAFLVPMGIWLLKSYLEKIPRELEEAAFMDGASRLYTLRRV 189

Query: 180 ILPLSVPAFVVVAIWQFTQIW-NEFLFAVTLTR-PESQPITVALAQLAGGEAVKWNLPMA 237
           +LPL+VP  +VV +  F   +  +FLFA+T     +  P+   + +  G ++VKWN  MA
Sbjct: 190 VLPLAVPGLIVVGVAVFLSAYAQQFLFAITFNSVKDYMPLPAGILEFIGYQSVKWNEMMA 249

Query: 238 GAILAALPTLLVYILLGRYFLRGLLAGSVK 267
            +I+  LP L++++ L RY + GL AG++K
Sbjct: 250 ASIVGILPVLVIFLFLQRYLVAGLTAGAIK 279


Lambda     K      H
   0.330    0.146    0.461 

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: 251
Number of extensions: 28
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: 268
Length of database: 280
Length adjustment: 25
Effective length of query: 243
Effective length of database: 255
Effective search space:    61965
Effective search space used:    61965
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 47 (22.7 bits)

This GapMind analysis is from Sep 24 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