GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mglB in Microvirga lotononidis WSM3557

Align glucose transporter, periplasmic substrate-binding component (characterized)
to candidate WP_085985143.1 MICLODRAFT_RS06940 sugar ABC transporter substrate-binding protein

Query= reanno::Phaeo:GFF3639
         (341 letters)



>NCBI__GCF_000262405.1:WP_085985143.1
          Length = 363

 Score =  129 bits (324), Expect = 1e-34
 Identities = 94/291 (32%), Positives = 143/291 (49%), Gaps = 31/291 (10%)

Query: 56  YVSADAQSSSAKQLSDIESLIAQGVDALIVLAQDAQAIGPAVQAAADEGIPVVAYDRLIE 115
           Y +ADA  S  +Q     S ++QG   +++   D+ A    V+ A  +GI V+AYDR I 
Sbjct: 77  YQNADANVS--RQQQQFNSAVSQGAKVIVLDPVDSAAAASLVKQAQGQGIKVIAYDRPIP 134

Query: 116 DGRA-FYLTFDNVEVGRMQARAVLEAQPSGNY--------VMIKGSPTDPNADFLRGGQQ 166
           D +A FY++FDN  +G+  A ++++     N         + I GSPTD  A  ++ G  
Sbjct: 135 DAKADFYVSFDNQAIGKSIADSLVQHLKKSNVTAGSGMGVLQINGSPTDAAAGLIKKG-- 192

Query: 167 EIIQAAIDSGDIKIVGEAYTDGWLPANAQRNMEQILTANDNKVDAVVASNDGTAGGVVAA 226
             I   +D+    I+ E  T  W P  AQ+     +T  +  +  VVA+NDGTAGG +AA
Sbjct: 193 --IHEGLDNSGYPILAEFDTPEWAPPKAQQWASGQITRFNKNILGVVAANDGTAGGAIAA 250

Query: 227 LTAQGMEGI-AVSGQDGDHAALNRVAKGTQTVSVWKDARDLGKAAANIAVEMAEGAVMGD 285
             A GM  +  V+G D   AAL  +  G Q  ++ K +  +  AAAN+A+++  G     
Sbjct: 251 FKAAGMNPVPPVTGNDATIAALQLIIAGDQYNTISKPSEIVAAAAANVAIQLLGGE---- 306

Query: 286 VAGGAAWTSPAGTEL---TARFLEPIPVTADNLSV-VVDAGWITKEALCQG 332
                  T  A T L    ++   P  +TADNL   +++    T E LC G
Sbjct: 307 -------TPKADTTLFNTPSKLFVPAVITADNLKAEIINKNINTAEQLCSG 350


Lambda     K      H
   0.313    0.128    0.362 

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: 223
Number of extensions: 13
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: 341
Length of database: 363
Length adjustment: 29
Effective length of query: 312
Effective length of database: 334
Effective search space:   104208
Effective search space used:   104208
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 49 (23.5 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