GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gltL in Dinoroseobacter shibae DFL-12

Align GluA aka CGL1950, component of Glutamate porter (characterized)
to candidate 3608728 Dshi_2120 ABC transporter related (RefSeq)

Query= TCDB::P48243
         (242 letters)



>FitnessBrowser__Dino:3608728
          Length = 376

 Score =  163 bits (413), Expect = 4e-45
 Identities = 99/238 (41%), Positives = 139/238 (58%), Gaps = 6/238 (2%)

Query: 1   MIKMTGVQKYFGDFHALTDIDLEIPRGQVVVVLGPSGSGKSTLCRTINRLETIEEGTIEI 60
           ++K   V K FG F A+   D EI RG+ + ++G SG GK+T  R +  LE   EG I +
Sbjct: 14  IVKFDNVVKRFGSFTAVKKADFEIGRGEFLAIMGSSGCGKTTTLRMLAGLEDPTEGAIYL 73

Query: 61  DGKVLPEEGKGLANLRADVGMVFQSFNLFPHLTIKDNVTLAPIKVRKMKKSEAEKLAMSL 120
           DG    E+  G A    D  MV+QS  LFP LT+++NV  A +K+R + K E  + A   
Sbjct: 74  DG----EQVNGKATWDRDTPMVWQSLALFPFLTVQENVEFA-LKMRGIGKEERRQRADKW 128

Query: 121 LERVGIANQADKYPAQLSGGQQQRVAIARALAMNPKIMLFDEPTSALDPEMVNEVLDVMA 180
           L+++ I   AD+   QLSGGQ+QRVA+ARAL   PKI+L DEP SALD  +   +  V++
Sbjct: 129 LDKMQITEFADRNINQLSGGQKQRVALARALVTEPKILLLDEPLSALDAHLKVRMQSVLS 188

Query: 181 SLAKE-GMTMVCVTHEMGFARKAADRVLFMADGLIVEDTEPDSFFTNPKSDRAKDFLG 237
           +L K+ G+T V VTH M  A   ADRV+ M+ G I +   P+  +  P +    +FLG
Sbjct: 189 NLQKDLGITFVYVTHSMSEAFSMADRVVIMSRGQIEQIGTPEEIYREPHNRFVAEFLG 246


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: 201
Number of extensions: 10
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: 376
Length adjustment: 27
Effective length of query: 215
Effective length of database: 349
Effective search space:    75035
Effective search space used:    75035
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: 48 (23.1 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