GapMind for catabolism of small carbon sources

 

Alignments for a candidate for RR42_RS28305 in Pseudomonas fluorescens FW300-N2E2

Align D-serine/D-alanine/glycine transporter (characterized, see rationale)
to candidate Pf6N2E2_1423 Gamma-aminobutyrate permease

Query= uniprot:A0A0C4YRF7
         (472 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1423
          Length = 466

 Score =  293 bits (750), Expect = 8e-84
 Identities = 155/423 (36%), Positives = 249/423 (58%), Gaps = 6/423 (1%)

Query: 19  LHRGLKDRHIQMIAIGGAIGVGLFLGAGRAIAIAGPGLMLSYAIGGVAIFFIMRALGELL 78
           L +G K RH+ M++I G IG GLF+G+G AIA AGP +ML+Y   G+ +  +MR LGE+ 
Sbjct: 13  LAQGFKPRHVTMLSIAGIIGAGLFVGSGHAIAAAGPAVMLAYLFSGLLVVLVMRMLGEMA 72

Query: 79  LYRPVSGSFATYAEEFVGPFAGFATGWSYWFMWVVTGMAEITAVAVYVHYWFPDVPQWIP 138
           +  P +GSF+TYA++ +G +AGF  GW YW+ WV+    E  A    ++ WFP +  W+ 
Sbjct: 73  VANPDTGSFSTYADQAIGRWAGFTIGWLYWWFWVLVIPIEALAAGHVLNQWFPAIDAWLF 132

Query: 139 ALATLAVLYLVNCVAVAVFGELEFWFALIKVVTIVAMIVIGLAIIFFGVTPLGPTASFSN 198
           A  ++ +L + N  +V+ +GE EFWFA+ KVV I+  I +G A++  G  P    +  S 
Sbjct: 133 ASVSIVLLAVTNLFSVSKYGEFEFWFAMAKVVAIIGFISLGFAVL-MGWIPEREASGLSR 191

Query: 199 LW-THGGFMPFGTLGVVLTLQIVMFAYQGVELIGVTAGEAQNPEKVLPHATNGVVWRILI 257
           L   HGGF P G   VV     +MF++ G E + + A E+ NP + +  AT  V+WRI +
Sbjct: 192 LMEEHGGFAPNGLSAVVGAFITIMFSFIGTEAVTIAAAESDNPAQNIAKATRSVIWRIGV 251

Query: 258 FYVGALIIMMALVPWNE-LKPGVSPFVYVFERIGVPGAAAIVNLVVITAAASSCNSGIFS 316
           FY+ ++ +++++VPWN+ L   V  +    E + +P A  +V++VV+ A AS  NS I+ 
Sbjct: 252 FYLLSIFVVISVVPWNDPLLASVGSYQRALELMNIPHAKFLVDMVVLIAVASCMNSSIYI 311

Query: 317 TGRMLYTLAQFGQAPRAFGRVSSKHVPSIAITFSAALMGIGV-LLNYIVPEQVFVWVTSI 375
             RMLY+L + G AP+A    SS  VP  A+  ++ ++G GV L +Y +P  +F ++ + 
Sbjct: 312 ASRMLYSLGRRGDAPKALKVTSSAGVPRSAV-IASTVLGAGVTLFSYFMPAGLFQFLLAS 370

Query: 376 SLVGSLWTWSIIMIAHLGYRKAIAAGRVKAVAFRMPGAPYANWLVVAFMIAVAVLLSLDP 435
           S   +L  + +I I+ L  R+ +    ++ + FRM   P+  WLV+ F+ A   ++ + P
Sbjct: 371 SGAIALLVYLVIAISQLRMRRMLQRQNIE-LPFRMWLFPWLTWLVIVFISAALAVMMVTP 429

Query: 436 GTR 438
             R
Sbjct: 430 EHR 432


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: 682
Number of extensions: 42
Number of successful extensions: 5
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: 466
Length adjustment: 33
Effective length of query: 439
Effective length of database: 433
Effective search space:   190087
Effective search space used:   190087
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