GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gtsA in Pseudovibrio axinellae Ad2

Align Sugar ABC transporter substrate-binding protein (characterized, see rationale)
to candidate WP_068006982.1 PsAD2_RS14045 carbohydrate ABC transporter substrate-binding protein

Query= uniprot:A0A165KPY4
         (416 letters)



>NCBI__GCF_001623255.1:WP_068006982.1
          Length = 413

 Score =  221 bits (562), Expect = 4e-62
 Identities = 134/411 (32%), Positives = 210/411 (51%), Gaps = 12/411 (2%)

Query: 4   MTKIAAVAVGLAAAMSASAGEVEVLHYWTSGGEAKSVAELKKIMQGKGHTWRDFAVAGGG 63
           +  +   A  LA+     A ++EV H+WTSGGEA +V      +   GHTW D A+AGG 
Sbjct: 4   LNALLVTAALLASTTFTQAADLEVTHWWTSGGEAAAVRVFADAVNNSGHTWVDSAIAGG- 62

Query: 64  GDSAMTVLKSRVISGNPPSAAQTK-GPAIQEWASEGVLANMDTLAKAEKWDELL-PKVVA 121
            D+A  V+ SR+  G+P  A Q   G   ++    G++ ++  +A+ E W +++ P  + 
Sbjct: 63  -DNARPVIISRISGGDPMQATQLNTGRDAEDLIRAGLMTDLTEVAEKEGWADIIRPAKLL 121

Query: 122 DVMKYKGAYVAAPVNVHRVNWMWGSSEALKKAGVAAMPKTWDEFFAAADKLKAAGLVPVA 181
           D  +Y+G     PVN+H   WMW + +  ++ G+A +P  W EF  +A  L+  G+ P+A
Sbjct: 122 DSCRYEGRIYCVPVNIHSFQWMWLNRKVYEQNGLA-VPTNWSEFVQSAPTLRDKGITPLA 180

Query: 182 HGGQNWQDFTTFESVVLGVGGAKFYQDALVKLDNTALTSDTMKKSLETFRRIKGYTDPGA 241
            GG+ WQ         + VGG   Y+    +    A +   M+K  + F   +   D G 
Sbjct: 181 VGGEPWQLSGMSGVFQVAVGGVDLYRKIKAQKSVEAASGPEMRKVFQAFADARDLGDNGH 240

Query: 242 PGRDWNLATAMLIQGKAGFQLMGDWAKGEFLAAGKAPGKDFLCAAAPGSANAFTFNVDSF 301
            GR WN AT+M+I GKA  Q+MGDWA+GEF  A +  GKD+ C    G         DSF
Sbjct: 241 VGRAWNNATSMVITGKAAAQIMGDWAQGEFSMAEQVAGKDYDCLPGLGMNPVLDTGGDSF 300

Query: 302 ILFKL--KDAAAQKAQSDLASSIMSPAFQEVFNLNKGSIPVRAGQPMDKFDDCAKASAKD 359
              K         KAQ ++AS ++S A Q  FNL KGS+PVR    ++  + C K   K 
Sbjct: 301 FFPKPVGDQPDVVKAQLEMASLLVSKAVQVDFNLKKGSLPVRGDVDLNAANSCMK---KG 357

Query: 360 FVDTAKSGGLVPSAAHGMAIAPATEGAIKDVVSQFWNDDKVSVADAMKKIA 410
               +    ++P  A   + +  T+G ++D+  +F+N  +++V +A  + A
Sbjct: 358 IAILSDPENILP--ATEQSFSSDTQGQLEDLWVEFFNAPEMTVDEAQARYA 406


Lambda     K      H
   0.315    0.128    0.383 

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: 466
Number of extensions: 28
Number of successful extensions: 7
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: 416
Length of database: 413
Length adjustment: 31
Effective length of query: 385
Effective length of database: 382
Effective search space:   147070
Effective search space used:   147070
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: 41 (21.6 bits)
S2: 50 (23.9 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