GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gltL in Pedobacter sp. GW460-11-11-14-LB5

Align PEB1C, component of Uptake system for glutamate and aspartate (characterized)
to candidate CA265_RS01140 CA265_RS01140 ABC transporter

Query= TCDB::A3ZI83
         (242 letters)



>FitnessBrowser__Pedo557:CA265_RS01140
          Length = 229

 Score =  142 bits (358), Expect = 6e-39
 Identities = 80/224 (35%), Positives = 133/224 (59%), Gaps = 11/224 (4%)

Query: 1   MIELKNVNKYYGTHH----VLKNINLSVKEGEKLVIIGPSGSGKSTTIRCMNGLEEVSSG 56
           ++ ++NV+K Y +      VL NIN S+  G  + I GPSGSGK+T +    GL+  SSG
Sbjct: 4   ILNIRNVSKIYQSAGRELTVLDNINFSITAGSTVAITGPSGSGKTTLLGLCAGLDRASSG 63

Query: 57  EVVVNNLVLNHKNKIE---ICRKYCAMVFQHFNLYPHMTVLQNLTLAPMKLQKKSKKEAE 113
            V +N + L   N+ E   +  +Y   +FQ+F L P +T L+N+ + P++L  +  K   
Sbjct: 64  TVELNGIALEKLNEDERAAVRNQYVGFIFQNFQLLPTLTALENV-MVPLEL--RGAKNIR 120

Query: 114 ETAFKYLKVVGLLDKANVYPATLSGGQQQRVAIARSLCTKKPYILFDEPTSALDPETIQE 173
             A + L  VGL D+++ YP  LSGG+QQRV++AR+   +   +  DEPT  LD ET ++
Sbjct: 121 AHALELLDKVGLADRSHHYPVQLSGGEQQRVSLARAFSNQPAILFADEPTGNLDAETSEK 180

Query: 174 VLDVMKEISHQSNTTMVVVTHEMGFAKEVADRIIFMEDGAIVEE 217
           V+ ++ +++  + TT+++VTH++  A   A R I ++ G I+ +
Sbjct: 181 VIKLLFDLNKDAGTTLIIVTHDLELAARTA-RSIKIKGGVIISD 223


Lambda     K      H
   0.317    0.133    0.372 

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: 127
Number of extensions: 7
Number of successful extensions: 3
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: 229
Length adjustment: 23
Effective length of query: 219
Effective length of database: 206
Effective search space:    45114
Effective search space used:    45114
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 (21.7 bits)
S2: 46 (22.3 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