GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hisP in Sphingomonas koreensis DSMZ 15582

Align BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized)
to candidate Ga0059261_3653 Ga0059261_3653 phosphate ABC transporter ATP-binding protein, PhoT family (TC 3.A.1.7.1)

Query= TCDB::P73721
         (252 letters)



>FitnessBrowser__Korea:Ga0059261_3653
          Length = 276

 Score =  136 bits (343), Expect = 4e-37
 Identities = 89/241 (36%), Positives = 139/241 (57%), Gaps = 17/241 (7%)

Query: 18  FGALQVLRGVTGEIYPKDVISIIGPSGCGKSTFLRCLNRL-EPISGGRLEVAGVDLSGAK 76
           +G  Q +R V+ ++  ++V + IGPSGCGKSTFLR LNR+ + ++  R+E   + L G  
Sbjct: 38  YGEKQAIRDVSIDVDMENVTAFIGPSGCGKSTFLRTLNRMNDTVASARVE-GEITLDGEN 96

Query: 77  IDQKHLR--QLRVRVGMVFQHFNLFPHLTVLQNLLLAPR----KVLRIPMAEAKDRALTY 130
           I  K +   QLR RVGMVFQ  N FP  ++ +N+   PR       +  M +  +R+L  
Sbjct: 97  IYDKSMDVVQLRARVGMVFQKPNPFPK-SIYENVAYGPRIHGLARAKGDMDQIVERSLK- 154

Query: 131 LDKVGLGTKA-DNYPDQ---LSGGQKQRVAIARGLCMKPEILLFDEPTSALDPELVGEVL 186
             + GL  +  D   D    LSGGQ+QR+ IAR + + PE++L DEP SALDP    ++ 
Sbjct: 155 --RAGLWEEVKDRLNDSGTALSGGQQQRLCIARAIAVDPEVILMDEPCSALDPIATAKIE 212

Query: 187 NVMKQLAEEGMTMAVVTHEMQFAREVSNRVFFFNQGIIEEEGDPNEVFRNPKSDRLRAFL 246
            ++ +L      + +VTH MQ A  VS R  FF+ G + E G+ +++F  P+ +R + ++
Sbjct: 213 ELIHELRGR-YAIVIVTHNMQQAARVSQRTAFFHLGTLVEYGETDQIFTAPRQERTKDYI 271

Query: 247 S 247
           +
Sbjct: 272 T 272


Lambda     K      H
   0.321    0.139    0.397 

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: 157
Number of extensions: 8
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: 252
Length of database: 276
Length adjustment: 25
Effective length of query: 227
Effective length of database: 251
Effective search space:    56977
Effective search space used:    56977
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 47 (22.7 bits)

This GapMind analysis is from Sep 17 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