GapMind for catabolism of small carbon sources

 

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

Align GluA aka CGL1950, component of Glutamate porter (characterized)
to candidate WP_047006469.1 AAW01_RS01810 phosphate ABC transporter ATP-binding protein

Query= TCDB::P48243
         (242 letters)



>NCBI__GCF_001010925.1:WP_047006469.1
          Length = 280

 Score =  141 bits (355), Expect = 2e-38
 Identities = 88/245 (35%), Positives = 136/245 (55%), Gaps = 12/245 (4%)

Query: 2   IKMTGVQKYFGDFHALTDIDLEIPRGQVVVVLGPSGSGKSTLCRTINRL-ETIE----EG 56
           ++  GV  Y+GD  A+ D+ ++I    V   +GPSG GKST  R +NR+ +TI     +G
Sbjct: 33  MRAQGVDVYYGDKRAIDDVSIDIYTEYVTAFIGPSGCGKSTFLRALNRMNDTIPSASVKG 92

Query: 57  TIEIDGKVLPEEGKGLANLRADVGMVFQSFNLFPHLTIKDNVTLAP-IKVRKMKKSEAEK 115
            IE+DG  +   G  +  LRA VGMVFQ  N FP  +I +N+   P I      +++ ++
Sbjct: 93  RIELDGDDIYASGMDVVQLRARVGMVFQKPNPFPK-SIYENIAYGPRIHGLAENRNDVDE 151

Query: 116 LAMSLLERVG----IANQADKYPAQLSGGQQQRVAIARALAMNPKIMLFDEPTSALDPEM 171
           +    L R G    + ++       LSGGQQQR+ IARA+A++P+++L DEP SALDP  
Sbjct: 152 IVEKSLRRAGLWEEVKDRLQDSGTALSGGQQQRLCIARAIAVDPEVILMDEPCSALDPIA 211

Query: 172 VNEVLDVMASLAKEGMTMVCVTHEMGFARKAADRVLFMADGLIVEDTEPDSFFTNPKSDR 231
             ++ +++  L +    +V VTH M  A + + R  F   G +VE       FTNP+  R
Sbjct: 212 TAKIEELIDEL-RGRYGIVIVTHSMQQAARVSQRTAFFHLGKMVEYGHTSDIFTNPREKR 270

Query: 232 AKDFL 236
            +D++
Sbjct: 271 TQDYI 275


Lambda     K      H
   0.319    0.135    0.379 

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: 155
Number of extensions: 11
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: 242
Length of database: 280
Length adjustment: 24
Effective length of query: 218
Effective length of database: 256
Effective search space:    55808
Effective search space used:    55808
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 (21.8 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