GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gtsD in Dyella japonica UNC79MFTsu3.2

Align ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized)
to candidate N515DRAFT_1085 N515DRAFT_1085 D-methionine transport system ATP-binding protein

Query= reanno::pseudo13_GW456_L13:PfGW456L13_1897
         (386 letters)



>FitnessBrowser__Dyella79:N515DRAFT_1085
          Length = 336

 Score =  131 bits (330), Expect = 2e-35
 Identities = 96/292 (32%), Positives = 149/292 (51%), Gaps = 29/292 (9%)

Query: 8   NVNKTY---GPGLPDTLKNIELKIDDGEFLILVGPSGCGKSTLMNCIAGLETISGGAILV 64
           +V+K+Y   G  +P  L+   L I DGE   ++G SG GKSTL+  I  LE  SGG+IL+
Sbjct: 6   DVHKSYRVDGKDIP-ALQPFSLDIADGEVFGIIGHSGAGKSTLIRLINLLERPSGGSILI 64

Query: 65  DDADISGMSP-----KDRDIAMVFQSYALYPTMSVRDNIAFGLKIR-KMPTAEIDEEVAR 118
           D  +++ +       + R I M+FQ + L  + +V DNIAF L++  +    +I   V  
Sbjct: 65  DGTEMTALGDAALRAQRRRIGMIFQHFNLLSSQTVADNIAFPLRLAGETDAGKIKARVDE 124

Query: 119 VSKLLQIEHLLSRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEM 178
           + + + +E   S+ P QLSGGQ+QRV + RALA RP I L DE  S LD +    +   +
Sbjct: 125 LLRRVGLEAHASKYPAQLSGGQKQRVGIARALANRPSILLCDEATSALDPQTTASVLELL 184

Query: 179 KLMHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKDIYNNPANLFVASFIGS 238
             +++ LK T V +TH+      + D+VAV+  G I + G   D++ +P +     F+  
Sbjct: 185 AEINRELKLTIVLITHEMDVVRRVCDRVAVLDAGRIVEHGAVADVFLHPRHPTTRRFVNE 244

Query: 239 ----------PPMNFIPLRLQRKDGRLLALLDSGQARCELPLG--MQDAGLE 278
                      P   +P       GR+L L   G+A     LG   +D G++
Sbjct: 245 ALPEEAAGELAPYTHVP-------GRILRLSFRGEATWTPALGRVARDTGVD 289


Lambda     K      H
   0.319    0.138    0.393 

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: 302
Number of extensions: 15
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: 386
Length of database: 336
Length adjustment: 29
Effective length of query: 357
Effective length of database: 307
Effective search space:   109599
Effective search space used:   109599
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 (21.7 bits)
S2: 49 (23.5 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