GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gtsA in Pseudovibrio axinellae Ad2

Align ABC transporter for D-Glucose-6-Phosphate, periplasmic substrate-binding component (characterized)
to candidate WP_068006982.1 PsAD2_RS14045 carbohydrate ABC transporter substrate-binding protein

Query= reanno::WCS417:GFF4324
         (428 letters)



>NCBI__GCF_001623255.1:WP_068006982.1
          Length = 413

 Score =  206 bits (525), Expect = 8e-58
 Identities = 140/416 (33%), Positives = 207/416 (49%), Gaps = 27/416 (6%)

Query: 1   MNAINRLAVAISIASLFPLSAFAADSKGTVEVVHWWTSGGEKAAVDVLKAQVEKDGFVWK 60
           M  +N L V  ++     L++        +EV HWWTSGGE AAV V    V   G  W 
Sbjct: 1   MKGLNALLVTAAL-----LASTTFTQAADLEVTHWWTSGGEAAAVRVFADAVNNSGHTWV 55

Query: 61  DGAVAGGGGATAMTVLKSRAVAGNPPGVAQIK-GPDIQEWASTGLLDTDVLKDVAKEEKW 119
           D A+AGG  A  + +  SR   G+P    Q+  G D ++    GL+ TD L +VA++E W
Sbjct: 56  DSAIAGGDNARPVII--SRISGGDPMQATQLNTGRDAEDLIRAGLM-TD-LTEVAEKEGW 111

Query: 120 -DSLLDKKVSDTVKYEGDYVAVPVNIHRVNWLWINPEVFKKAGITKNPTTLQEFYAAGDK 178
            D +   K+ D+ +YEG    VPVNIH   W+W+N +V+++ G+   PT   EF  +   
Sbjct: 112 ADIIRPAKLLDSCRYEGRIYCVPVNIHSFQWMWLNRKVYEQNGLAV-PTNWSEFVQSAPT 170

Query: 179 LKAAGFIPLAHGGQPWQDSTVFEAVVLSVMGADGYKKALVDLDNGALTGPEMVKALTELK 238
           L+  G  PLA GG+PWQ S +     ++V G D Y+K        A +GPEM K      
Sbjct: 171 LRDKGITPLAVGGEPWQLSGMSGVFQVAVGGVDLYRKIKAQKSVEAASGPEMRKVFQAFA 230

Query: 239 KVATYMDVDGKGQDWNLEAGKVINGKAGMQIMGDWAKSEWTAAKKVAGKDYECVAFPGTD 298
                 D    G+ WN     VI GKA  QIMGDWA+ E++ A++VAGKDY+C+   G +
Sbjct: 231 DARDLGDNGHVGRAWNNATSMVITGKAAAQIMGDWAQGEFSMAEQVAGKDYDCLPGLGMN 290

Query: 299 KAFTYNIDSLAVFKQKDKG----TAAGQQDIAKVVLGENFQKVFSINKGSIPVRNDMLNK 354
                  DS   F  K  G        Q ++A +++ +  Q  F++ KGS+PVR D    
Sbjct: 291 PVLDTGGDSF--FFPKPVGDQPDVVKAQLEMASLLVSKAVQVDFNLKKGSLPVRGD---- 344

Query: 355 MDSYGFDSCAQTAAKDFLADAKTGGLQPSMAHNMATTLAVQGAFFDVVTNYINDPK 410
           +D    +SC +      L+D +   + P+   + ++    QG   D+   + N P+
Sbjct: 345 VDLNAANSCMKKGIA-ILSDPE--NILPATEQSFSSD--TQGQLEDLWVEFFNAPE 395


Lambda     K      H
   0.314    0.131    0.388 

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: 487
Number of extensions: 21
Number of successful extensions: 4
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: 428
Length of database: 413
Length adjustment: 32
Effective length of query: 396
Effective length of database: 381
Effective search space:   150876
Effective search space used:   150876
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: 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