GapMind for catabolism of small carbon sources

 

Alignments for a candidate for musK in Phaeacidiphilus oryzae TH49

Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate WP_037573817.1 BS73_RS18100 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC

Query= BRENDA::Q8NMV1
         (376 letters)



>NCBI__GCF_000744815.1:WP_037573817.1
          Length = 369

 Score =  437 bits (1123), Expect = e-127
 Identities = 230/377 (61%), Positives = 276/377 (73%), Gaps = 12/377 (3%)

Query: 1   MATVTFKDASLSYPGAKEPTVKKFNLEIADGEFLVLVGPSGCGKSTTLRMLAGLENVTDG 60
           MATVT+  A+  YPG  +P V   +LEIADGEFLVLVGPSGCGKST+LRMLAGLE+V +G
Sbjct: 1   MATVTYDKATRIYPGGDKPAVDALDLEIADGEFLVLVGPSGCGKSTSLRMLAGLEDVNNG 60

Query: 61  AIFIGDKDVTHVAPRDRDIAMVFQNYALYPHMTVGENMGFALKIAGKSQDEINKRVDEAA 120
           AI IG++DVTH+ P+DRDIAMVFQNYALYPHMTV +NMGFALKIAG ++ EI  +V+EAA
Sbjct: 61  AIRIGERDVTHLPPKDRDIAMVFQNYALYPHMTVADNMGFALKIAGVNKAEIRSKVEEAA 120

Query: 121 ATLGLTEFLERKPKALSGGQRQRVAMGRAIVRNPQVFLMDEPLSNLDAKLRVQTRTQIAA 180
             L LTEFL+RKPKALSGGQRQRVAMGRAIVR PQVFLMDEPLSNLDAKLRV TRTQIA 
Sbjct: 121 KILDLTEFLDRKPKALSGGQRQRVAMGRAIVREPQVFLMDEPLSNLDAKLRVSTRTQIAG 180

Query: 181 LQRKLGVTTVYVTHDQTEALTMGDRIAVLKDGYLQQVGAPRELYDRPANVFVAGFIGSPA 240
           LQR+LG+TTVYVTHDQ EA+TMGDR+AVLKDG LQQV  PR +YDRPAN+FVAGFIGSPA
Sbjct: 181 LQRRLGITTVYVTHDQVEAMTMGDRVAVLKDGLLQQVDTPRNMYDRPANLFVAGFIGSPA 240

Query: 241 MNLGTFSVKDGDATSGHARIKLSPETLAAMTPEDNGRITIGFRPEALEII--PEGESTDL 298
           MNL    + DG    G + +++S + +       +  +T+G RPE L+I+   EG   D 
Sbjct: 241 MNLVEVPITDGGVKFGESVVQVSRDAVGEAANAGDKTVTVGVRPEHLDIVGGTEGGGEDK 300

Query: 299 SIPIKLDFVEELGSDSFLYGKLVGEGDLGSSSEDVPESGQIVVRAAPNAAPAPGSVFHAR 358
            + + ++ VEELG+D ++YG          S++   E+  +VVR      P  G      
Sbjct: 301 GLAVTVNVVEELGADGYVYG----------SAKVGTETIDLVVRVGGRDIPMKGDQLRVV 350

Query: 359 IVEGGQHNFSASTGKRL 375
              G  H FS STGKRL
Sbjct: 351 PRAGETHVFSTSTGKRL 367


Lambda     K      H
   0.316    0.135    0.380 

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: 497
Number of extensions: 17
Number of successful extensions: 3
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: 376
Length of database: 369
Length adjustment: 30
Effective length of query: 346
Effective length of database: 339
Effective search space:   117294
Effective search space used:   117294
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 Apr 09 2024. 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