GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Pf6N2E2_5402 in Marinobacter adhaerens HP15

Align ABC transporter for D-Alanine, periplasmic substrate-binding component (characterized)
to candidate GFF2246 HP15_2196 glutamate/glutamine/aspartate/asparagine ABC transporter, periplasmic substrate-binding protein

Query= reanno::pseudo6_N2E2:Pf6N2E2_5402
         (343 letters)



>FitnessBrowser__Marino:GFF2246
          Length = 347

 Score =  410 bits (1054), Expect = e-119
 Identities = 208/344 (60%), Positives = 252/344 (73%), Gaps = 4/344 (1%)

Query: 1   MKLLKS-TLAVMTAAAVLGVSGFAQAGATLDAVQKKGFVQCGVSDGLPGFSVPDSTGKIV 59
           M+  KS  L +  A      +G A A  TL+ V++KG +QCGV+ GLPGFS PD  G   
Sbjct: 7   MRKTKSIALGIALAVGTFSATG-AMAATTLENVKEKGHLQCGVTSGLPGFSQPDEKGNWT 65

Query: 60  GIDADFCRAVAAAVFGDATKVKFSQLNAKERFTALQSGEIDMLSRNSTMTSSRDAGMGLK 119
           GID D CRAVAAA+FGDA  V+F+ L AKERFTALQSGEIDMLSRN+T T +RDA +GL 
Sbjct: 66  GIDVDTCRAVAAAIFGDANAVEFTPLTAKERFTALQSGEIDMLSRNTTWTLTRDASLGLN 125

Query: 120 FPGFITYYDGIGFLANNKLGVKSAKELDGATICIQAGTTTELNVSDYFRANGLKYTPITF 179
           F G + YYDG GFL N  +GV  A +LDGATICIQAGTTTELN+SDYFRA G+++ PI F
Sbjct: 126 FAG-VNYYDGQGFLINKGIGVDDATQLDGATICIQAGTTTELNLSDYFRAKGMEFKPIVF 184

Query: 180 DTSDESAKSLESGRCDVLTSDKSQLFAQRSKLASPKDYVVLPETISKEPLGPVVRNGDDE 239
           DTS+++ +   +GRCDVLTSD+SQL A RSKL+ P    +LP TISKEPLGPVVR GDD+
Sbjct: 185 DTSEQTVQGFAAGRCDVLTSDRSQLAALRSKLSDPSSAKILPNTISKEPLGPVVRQGDDQ 244

Query: 240 WLAIVRWTGYALLNAEEAGVTSKNVEAEAKSTKNPDVARMLGADGEYGKDLKLPKDWVVQ 299
           W  IV+W  +A +NAEE GVTS N +   KS  NP++ R+LG DG+ G  L LP D+  Q
Sbjct: 245 WFNIVKWVLFAQINAEELGVTSANADDMLKS-DNPNIQRLLGTDGDMGAKLGLPDDFGYQ 303

Query: 300 IVKQVGNYGEMFERNLGKGTPLEIDRGLNALWNAGGIQYAPPVR 343
            VK VGNYGEM++RN+G  TPL +DRG+NALW  GGI YAPPVR
Sbjct: 304 AVKLVGNYGEMYDRNVGPDTPLGLDRGINALWTEGGIMYAPPVR 347


Lambda     K      H
   0.315    0.133    0.383 

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: 440
Number of extensions: 19
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: 343
Length of database: 347
Length adjustment: 29
Effective length of query: 314
Effective length of database: 318
Effective search space:    99852
Effective search space used:    99852
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: 42 (22.0 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