GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PLT5 in Sphingomonas koreensis DSMZ 15582

Align polyol transporter 5 (characterized)
to candidate Ga0059261_1777 Ga0059261_1777 MFS transporter, sugar porter (SP) family

Query= CharProtDB::CH_091483
         (539 letters)



>FitnessBrowser__Korea:Ga0059261_1777
          Length = 458

 Score =  218 bits (556), Expect = 3e-61
 Identities = 146/459 (31%), Positives = 236/459 (51%), Gaps = 41/459 (8%)

Query: 43  ASMTSILLGYDIGVMSGAMIYIKRDLKINDLQIGILAGSLNIYSLIGSCAAGRTSDWIGR 102
           A++  +L G+D  V+SGA   ++    + D  +G    S  I +++GS  AG  +D  GR
Sbjct: 29  AALGGLLFGFDTAVISGATQALQLQFGLTDAMLGFTVASALIGTVLGSLIAGAPADRFGR 88

Query: 103 RYTIVLAGAIFFAGAILMGLSPNY-AFLMFGRFIAGIGVGYALMIAPVYTAEVSPASSRG 161
           +  ++     +   ++  GL+P+  AFL+F RF+ G+ +G A ++ P+Y AEVSPA  RG
Sbjct: 89  KGVMLTVAIAYVVSSLGTGLAPDLNAFLVF-RFMGGLAIGAASVVTPIYIAEVSPARFRG 147

Query: 162 FLNSFPEVFINAGIMLGYVSNLAFSNL-PLKVGWRLMLGIGAVPSVILAIGVLAMPESPR 220
            L +  ++ I  GI++ ++SN   + L    V WR M GI AVPS I  +  L +PESPR
Sbjct: 148 RLVAMNQLNIVLGILIAFLSNYIIAGLVQYDVAWRWMFGIVAVPSTIFLLVTLLLPESPR 207

Query: 221 WLVMQGRLGDAKRVLDKTSDSPTEATLR----LEDIKHAAGIPADCHDDVVQVSRRNSHG 276
           WL + G+   A+ V+ +   +   A L      E  + AAG P        ++ +R+   
Sbjct: 208 WLAIHGQADRARDVMQRLGFADPRAELARIELAEAREEAAGKP--------RLFQRSHF- 258

Query: 277 EGVWRELLIRPTPAVRRVMIAAIGIHFFQQASGIDAVVLFSPRIFKTAGLKTDHQQLLAT 336
                      TP     +  AI I  F Q SGI+A++ ++PRIF+ AG   D   LL +
Sbjct: 259 -----------TP-----VACAIAIAMFNQLSGINALLYYAPRIFELAGAGAD-SALLQS 301

Query: 337 VAVGVVKTSFILVATFLLDRIGRRPLLLTSVGGMVLSLAALGTSLTIIDQSEKKVMWAVV 396
           +AVG     F + A FL+DR GRRPLL         +L  +G  L         +++   
Sbjct: 302 IAVGGTNLVFTVAALFLIDRFGRRPLLFVGSVICAATLLLVGWQLESAKPDGTLILFG-- 359

Query: 397 VAIATVMTYVATFSIGAGPITWVYSSEIFPLRLRSQGSSMGVVVNRVTSGVISISFLPMS 456
                ++ ++A F++  G + WV+ SE+FP  +R +G ++G   + V +  I+ +F P+ 
Sbjct: 360 -----LLGFIAAFAMSQGAVIWVFISEVFPSAVRGKGQALGSTTHWVMAAAITWAF-PVF 413

Query: 457 KAMTTGGAFYLFGGIATVAWVFFYTFLPETQGRMLEDMD 495
            A   G  F  FG +  +  ++ + F+PET G  LEDM+
Sbjct: 414 AASVGGWVFAFFGAMMLLQLLWTWKFMPETNGIALEDMN 452


Lambda     K      H
   0.322    0.137    0.410 

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: 698
Number of extensions: 32
Number of successful extensions: 7
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: 539
Length of database: 458
Length adjustment: 34
Effective length of query: 505
Effective length of database: 424
Effective search space:   214120
Effective search space used:   214120
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 (21.9 bits)
S2: 52 (24.6 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