GapMind for catabolism of small carbon sources

 

Alignments for a candidate for musK in Pseudomonas stutzeri RCH2

Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate GFF1860 Psest_1899 ABC-type sugar transport systems, ATPase components

Query= BRENDA::Q8NMV1
         (376 letters)



>FitnessBrowser__psRCH2:GFF1860
          Length = 390

 Score =  299 bits (766), Expect = 8e-86
 Identities = 166/380 (43%), Positives = 231/380 (60%), Gaps = 20/380 (5%)

Query: 1   MATVTFKDASLSYPGAKEPTVKKFNLEIADGEFLVLVGPSGCGKSTTLRMLAGLENVTDG 60
           MA++  ++   SY  ++  T+K   L+I  GEFL+LVGPSGCGKST +  +AGLEN+T G
Sbjct: 1   MASLELRNVQKSYGNSQIATLKDIALKIDAGEFLILVGPSGCGKSTLMNCIAGLENITGG 60

Query: 61  AIFIGDKDVTHVAPRDRDIAMVFQNYALYPHMTVGENMGFALKIAGKSQDEINKRVDEAA 120
            I +  +D++  +P+DRDIAMVFQ+YALYP M+V +N+ F LK+      +I + V   A
Sbjct: 61  EILVDGEDISQASPKDRDIAMVFQSYALYPTMSVRDNIAFGLKMRKVPAAKIEEEVARVA 120

Query: 121 ATLGLTEFLERKPKALSGGQRQRVAMGRAIVRNPQVFLMDEPLSNLDAKLRVQTRTQIAA 180
             L +   LERKP  LSGGQ+QRVAMGRA+ R P+++L DEPLSNLDAKLRV+ RT+I  
Sbjct: 121 KLLQIEPLLERKPSQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEIKL 180

Query: 181 LQRKLGVTTVYVTHDQTEALTMGDRIAVLKDGYLQQVGAPRELYDRPANVFVAGFIGSPA 240
           + ++L  TTVYVTHDQ EA+T+GD++AV+KDG +QQ G P E+Y+ PAN+FVA FIGSP 
Sbjct: 181 MHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGVIQQFGTPHEIYNNPANLFVASFIGSPP 240

Query: 241 MNLGTFSV--KDGDATSGHARIKLSPETLAAMTPEDNGR---ITIGFRPEALEIIPEGES 295
           MN     +  +DG         + S E    +T +D  R   + +G RPE + + P G S
Sbjct: 241 MNFVPLRIRQRDGRWVGVLNSEQGSCELPLPITSDDGLRDRELILGIRPEQIGLAPAG-S 299

Query: 296 TDLSIPIKLDFVEELGSDSFLYGKLVGEGDLGSSSEDVPESGQIVVRAAPNAAPAPGSVF 355
            D S+ + ++ VE  G D+ +   L                 +   R AP+ AP  G   
Sbjct: 300 ADFSLAVDIEVVEPTGPDTLVVFTL--------------NQVKACCRLAPDQAPRVGETL 345

Query: 356 HARIVEGGQHNFSASTGKRL 375
           + +        F A TG+RL
Sbjct: 346 NLQFDPRRALLFDAQTGERL 365


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: 395
Number of extensions: 11
Number of successful extensions: 1
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: 390
Length adjustment: 30
Effective length of query: 346
Effective length of database: 360
Effective search space:   124560
Effective search space used:   124560
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 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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