GapMind for catabolism of small carbon sources

 

Alignments for a candidate for musK in Halomonas xinjiangensis TRM 0175

Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate WP_043527041.1 JH15_RS03500 sn-glycerol-3-phosphate import ATP-binding protein UgpC

Query= BRENDA::Q8NMV1
         (376 letters)



>NCBI__GCF_000759345.1:WP_043527041.1
          Length = 354

 Score =  314 bits (805), Expect = 2e-90
 Identities = 183/374 (48%), Positives = 233/374 (62%), Gaps = 26/374 (6%)

Query: 1   MATVTFKDASLSYPGAKEPTVKKFNLEIADGEFLVLVGPSGCGKSTTLRMLAGLENVTDG 60
           MA++       +Y G  E  VK  +LEIADGEF+VLVGPSGCGKST LRM+AGLE +TDG
Sbjct: 1   MASIQLTGLKKTYAGNVE-AVKGIDLEIADGEFVVLVGPSGCGKSTLLRMVAGLETITDG 59

Query: 61  AIFIGDKDVTHVAPRDRDIAMVFQNYALYPHMTVGENMGFALKIAGKSQDEINKRVDEAA 120
            + I D+ V  + P +RDIAMVFQNYALYPHMTV  N+ + LK  G  ++EI +RV +AA
Sbjct: 60  TLKIDDRVVNDLEPAERDIAMVFQNYALYPHMTVFGNLAYGLKNRGVKREEIERRVHDAA 119

Query: 121 ATLGLTEFLERKPKALSGGQRQRVAMGRAIVRNPQVFLMDEPLSNLDAKLRVQTRTQIAA 180
           A L +  FLERKP+ LSGGQRQRVAMGRA+VR P  FL DEPLSNLDAKLRVQ R +I  
Sbjct: 120 AMLEIEPFLERKPRKLSGGQRQRVAMGRALVREPSAFLFDEPLSNLDAKLRVQMRVEIKQ 179

Query: 181 LQRKLGVTTVYVTHDQTEALTMGDRIAVLKDGYLQQVGAPRELYDRPANVFVAGFIGSPA 240
           LQR+L  T++YVTHDQ EALT+GDR+ VL  G ++QVG P E+Y++PA++FVA FIGSPA
Sbjct: 180 LQRRLKTTSLYVTHDQLEALTLGDRLVVLNGGSIEQVGTPMEVYEKPASMFVATFIGSPA 239

Query: 241 MNLGTFSVKDGDATSGHARIKLSPETLAAMTPEDNGRITIGFRPEALEIIPEGESTDLSI 300
           MN+   +       +G        + LAA T        IG RP+ L I    E   L +
Sbjct: 240 MNMLPVAYLRERGANGLL------DHLAADTD------VIGIRPDDLRIEAPDED-HLVV 286

Query: 301 PIKLDFVEELGSDSFLYGKLVGEGDLGSSSEDVPESGQIVVRAAPNAAPAPGSVFHARIV 360
              ++  E  G++S LY  L G         D P     V+R +     A G      ++
Sbjct: 287 TGTVELFEAAGAESHLYVSLEG--------SDQP----TVIRTSARPPVAEGETMRFHVL 334

Query: 361 EGGQHNFSASTGKR 374
               H F+ ++GKR
Sbjct: 335 PSALHPFNQASGKR 348


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: 344
Number of extensions: 7
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: 376
Length of database: 354
Length adjustment: 30
Effective length of query: 346
Effective length of database: 324
Effective search space:   112104
Effective search space used:   112104
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: 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