GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fruP in Echinicola vietnamensis KMM 6221, DSM 17526

Align MFS transporter, FHS family, L-fucose permease (characterized, see rationale)
to candidate Echvi_0508 Echvi_0508 L-fucose:H+ symporter permease

Query= uniprot:A0A1I2JXG1
         (442 letters)



>FitnessBrowser__Cola:Echvi_0508
          Length = 431

 Score =  254 bits (649), Expect = 4e-72
 Identities = 154/438 (35%), Positives = 247/438 (56%), Gaps = 19/438 (4%)

Query: 9   PSKTSLPGAARERYTDYPMAMGVLTSIFFMWGFLTCLNDILIPHLKAVFKLNYAEAMLVQ 68
           PSK++L   A    T +P  +  LTS+F +WG    + D L+   K +  +   +   +Q
Sbjct: 4   PSKSALVSKA----TLWPFIL--LTSLFLLWGLANNMTDTLLAAFKKILSMTDTQTSFIQ 57

Query: 69  FTFFGAYFLMSLPAGLLVARLGYKKGIVAGLAVAGVGAAGFWPAAAMHFYPAFLGALFVL 128
             F+GAYF ++LPA + + +  YK G++ GL +  VG   F+PA+    Y  FL AL+VL
Sbjct: 58  LAFYGAYFCLALPAAIYIKKYTYKSGVLLGLGLFAVGGLLFYPASITMSYGFFLFALYVL 117

Query: 129 ATGITVLQVAANAYVALLGPEKSASSRLTLAQALNSLGTFLAPKFGGLLILSAA-VLSAE 187
           A G+++L+ +AN Y+ ++GPE SA+ RL LAQ+ N +G+ +        ILS   V  A+
Sbjct: 118 AGGLSILETSANPYIMVMGPEASATRRLNLAQSFNPVGSIIGVVLSKFFILSKLNVAEAD 177

Query: 188 QIAKLSPAEQVAYRVQEAQTVQGPYLGLAIVLFLLAVFVYLFRLPALTEKTEQASVKQHS 247
           + ++++  +    R +E   V G Y+G+A+ L ++ V +   ++P  +E   Q S+  + 
Sbjct: 178 ERSRMTAEQLQQVRQEELDAVMGTYVGVALFLVVMWVLIKFTKMPTASEGGLQDSL-GNG 236

Query: 248 LVSPLRHPHVLFGVLAIFFYVGGEVAIGSFLVNYLSMPDIGNMSEQAAANWVAYYWLGAM 307
           L   L + + +FGVLA FFYVG ++ I S+ + Y+ M    +M+E  A+N    Y+L A+
Sbjct: 237 LKRLLGNKNYVFGVLAQFFYVGAQIGIWSYTIRYVMME--LDMNESDASN----YYLAAI 290

Query: 308 ----IGRFIGSALLAKLSPRKLLAIFAAINMALVLTTMMTKGTVAMYSVVSIGLFNSIMF 363
               + RF+ +AL+  + P  L+AI A   + L +  +   G V   ++V I    S+MF
Sbjct: 291 VLFTVSRFLFTALMKFVRPSLLMAISAIGAIGLTMVVIFGHGMVGSIALVCISGCMSLMF 350

Query: 364 PTIFSLGIERMGPMTGEASSLLIMAIVGGAIVPFVQGLFADHIGVQH-AFFLPLLCYAYI 422
           PTI+ L  E +G  T    S LIMAI+GGAI PF+QGL +D +   H +FF+P  CY  +
Sbjct: 351 PTIYGLAAEGLGDDTKLGGSGLIMAILGGAIFPFIQGLVSDSLDSIHLSFFVPAACYLVV 410

Query: 423 VFYGLYGSRIKSDTPVAA 440
           V YGL+  + K + P  A
Sbjct: 411 VAYGLFHYKHKKEIPAMA 428


Lambda     K      H
   0.327    0.140    0.414 

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: 477
Number of extensions: 23
Number of successful extensions: 4
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: 442
Length of database: 431
Length adjustment: 32
Effective length of query: 410
Effective length of database: 399
Effective search space:   163590
Effective search space used:   163590
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 (21.7 bits)
S2: 51 (24.3 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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