GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bgtA in Erythrobacter gangjinensis K7-2

Align BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized)
to candidate WP_047006469.1 AAW01_RS01810 phosphate ABC transporter ATP-binding protein

Query= TCDB::P73721
         (252 letters)



>NCBI__GCF_001010925.1:WP_047006469.1
          Length = 280

 Score =  135 bits (339), Expect = 1e-36
 Identities = 91/243 (37%), Positives = 139/243 (57%), Gaps = 21/243 (8%)

Query: 18  FGALQVLRGVTGEIYPKDVISIIGPSGCGKSTFLRCLNRLE---PISG--GRLEVAGVDL 72
           +G  + +  V+ +IY + V + IGPSGCGKSTFLR LNR+    P +   GR+E+ G D+
Sbjct: 42  YGDKRAIDDVSIDIYTEYVTAFIGPSGCGKSTFLRALNRMNDTIPSASVKGRIELDGDDI 101

Query: 73  SGAKIDQKHLRQLRVRVGMVFQHFNLFPHLTVLQNLLLAPR----KVLRIPMAEAKDRAL 128
             + +D   + QLR RVGMVFQ  N FP  ++ +N+   PR       R  + E  +++L
Sbjct: 102 YASGMD---VVQLRARVGMVFQKPNPFPK-SIYENIAYGPRIHGLAENRNDVDEIVEKSL 157

Query: 129 TYLDKVGLGTKA-DNYPDQ---LSGGQKQRVAIARGLCMKPEILLFDEPTSALDPELVGE 184
               + GL  +  D   D    LSGGQ+QR+ IAR + + PE++L DEP SALDP    +
Sbjct: 158 R---RAGLWEEVKDRLQDSGTALSGGQQQRLCIARAIAVDPEVILMDEPCSALDPIATAK 214

Query: 185 VLNVMKQLAEEGMTMAVVTHEMQFAREVSNRVFFFNQGIIEEEGDPNEVFRNPKSDRLRA 244
           +  ++ +L      + +VTH MQ A  VS R  FF+ G + E G  +++F NP+  R + 
Sbjct: 215 IEELIDELRGR-YGIVIVTHSMQQAARVSQRTAFFHLGKMVEYGHTSDIFTNPREKRTQD 273

Query: 245 FLS 247
           +++
Sbjct: 274 YIT 276


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: 175
Number of extensions: 9
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: 280
Length adjustment: 25
Effective length of query: 227
Effective length of database: 255
Effective search space:    57885
Effective search space used:    57885
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 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