GapMind for catabolism of small carbon sources

 

Alignments for a candidate for RR42_RS28305 in Dyella japonica UNC79MFTsu3.2

Align D-serine/D-alanine/glycine transporter (characterized, see rationale)
to candidate N515DRAFT_2630 N515DRAFT_2630 amino acid/polyamine/organocation transporter, APC superfamily

Query= uniprot:A0A0C4YRF7
         (472 letters)



>FitnessBrowser__Dyella79:N515DRAFT_2630
          Length = 454

 Score =  523 bits (1347), Expect = e-153
 Identities = 249/437 (56%), Positives = 322/437 (73%)

Query: 19  LHRGLKDRHIQMIAIGGAIGVGLFLGAGRAIAIAGPGLMLSYAIGGVAIFFIMRALGELL 78
           L RGL++RHI+++A+G AIGVGLFLG+  AI +AGP ++LSY +GGVAIF IMRALGE+ 
Sbjct: 7   LQRGLQERHIRLMALGSAIGVGLFLGSANAIRLAGPAILLSYLLGGVAIFIIMRALGEMA 66

Query: 79  LYRPVSGSFATYAEEFVGPFAGFATGWSYWFMWVVTGMAEITAVAVYVHYWFPDVPQWIP 138
           +  PV+GSF+ YA++++GP  G+ TGW+YWFMW++T +AEITAV VY+  WFPDVPQWI 
Sbjct: 67  VQNPVAGSFSRYAQDYLGPLPGYLTGWNYWFMWLMTCIAEITAVGVYMGVWFPDVPQWIW 126

Query: 139 ALATLAVLYLVNCVAVAVFGELEFWFALIKVVTIVAMIVIGLAIIFFGVTPLGPTASFSN 198
           ALA L  +  VN  AV  +GE EFWFA+IKVVTIV MIV G A+I FG+   G     SN
Sbjct: 127 ALAALVTMGAVNLAAVKAYGEFEFWFAMIKVVTIVLMIVGGGAMIVFGLGNQGVPTGISN 186

Query: 199 LWTHGGFMPFGTLGVVLTLQIVMFAYQGVELIGVTAGEAQNPEKVLPHATNGVVWRILIF 258
           LWTHGGFMP G  G+++ LQ+VMFAY GVE+IG+TAGEA NP+K +P A N V WRILIF
Sbjct: 187 LWTHGGFMPNGAKGMLMALQMVMFAYLGVEMIGLTAGEADNPKKSIPDAINSVFWRILIF 246

Query: 259 YVGALIIMMALVPWNELKPGVSPFVYVFERIGVPGAAAIVNLVVITAAASSCNSGIFSTG 318
           YVGAL ++M++ PWNEL    SPFV  FER+G+  AA I+N VV+TAA SSCN GI+STG
Sbjct: 247 YVGALFVIMSIYPWNELGTHGSPFVMTFERLGIKSAAGIINFVVLTAALSSCNGGIYSTG 306

Query: 319 RMLYTLAQFGQAPRAFGRVSSKHVPSIAITFSAALMGIGVLLNYIVPEQVFVWVTSISLV 378
           RML+ LAQ GQAPR F   S   +P+ A+  S   +  GVLLNY+VP +VFVWVTS +  
Sbjct: 307 RMLFNLAQQGQAPRTFAVTSPSGIPNRAVLVSLVALLFGVLLNYLVPAKVFVWVTSAATF 366

Query: 379 GSLWTWSIIMIAHLGYRKAIAAGRVKAVAFRMPGAPYANWLVVAFMIAVAVLLSLDPGTR 438
           G++WTW I++I  + YR+ ++  +   + FRMP  PYA++L +AF++ V  L+   P TR
Sbjct: 367 GAIWTWGIVLITQMKYRRGLSEAQRSQLVFRMPFFPYASYLALAFLVLVVGLMGYFPDTR 426

Query: 439 VALYVAPVWFALLGIGY 455
           VAL V P+W  LL + Y
Sbjct: 427 VALIVGPLWLVLLTVLY 443


Lambda     K      H
   0.328    0.142    0.445 

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: 783
Number of extensions: 45
Number of successful extensions: 1
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: 472
Length of database: 454
Length adjustment: 33
Effective length of query: 439
Effective length of database: 421
Effective search space:   184819
Effective search space used:   184819
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 51 (24.3 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