GapMind for catabolism of small carbon sources

 

Alignments for a candidate for MFS-glucose in Gallaecimonas xiamenensis 3-C-1

Align Glucose/galactose porter (characterized)
to candidate WP_008482148.1 B3C1_RS00390 sugar MFS transporter

Query= TCDB::P0C105
         (412 letters)



>NCBI__GCF_000299915.1:WP_008482148.1
          Length = 424

 Score =  558 bits (1438), Expect = e-163
 Identities = 284/425 (66%), Positives = 335/425 (78%), Gaps = 15/425 (3%)

Query: 1   MATSIPTNNPLHTETSSQKNYGFALTSLTLLFFMWGFITCLNDILIPHLKNVFQLNYTQS 60
           MA ++P  N     +   + Y FALTS+T LFFM GFITCLNDILIPHLKNVF LNYTQ+
Sbjct: 1   MAGALP--NTAQATSQEHQGYTFALTSMTFLFFMMGFITCLNDILIPHLKNVFSLNYTQA 58

Query: 61  MLIQFCFFGAYFIVSLPAGQLVKRISYKRGIVVGLIVAAIGCALFIPAASYRVYALFLGA 120
           MLIQFCFFGAYF+VS PAG L +R+ YK  +V+ L+V+AIGC LFI AASYRVY LFLGA
Sbjct: 59  MLIQFCFFGAYFVVSYPAGALARRLGYKWALVISLVVSAIGCLLFITAASYRVYELFLGA 118

Query: 121 LFVLASGVTILQVAANPYVTILGKPETAASRLTLTQAFNSLGTTVAPVFGAVLILSAAT- 179
           LF+LASGVT LQVA NPYVT+LGKPETA++RLTL QAFNSLGTT+AP FGA+LIL AAT 
Sbjct: 119 LFILASGVTTLQVAVNPYVTVLGKPETASARLTLNQAFNSLGTTLAPTFGAMLILGAATA 178

Query: 180 ----------DATVNAEADAVRFPYLLLALAFTVLAIIFAILKPPDVQEDEPALSDKKE- 228
                      A   +EADAV+FPYLLLA  F VLA + A LK PD++E + A + +   
Sbjct: 179 DFTGLSQEQVTALRLSEADAVKFPYLLLASTFLVLAAVLAYLKLPDMREQDNAAAAQASQ 238

Query: 229 -GSAWQYRHLVLGAIGIFVYVGAEVSVGSFLVNFLSDPTVAGLSETDAAHHVAYFWGGAM 287
            GSAWQYRHLVLGA+G+FVYVGAEVS+GS LVNFL +  +AGL+E DAAH+V+Y+WGGAM
Sbjct: 239 GGSAWQYRHLVLGALGLFVYVGAEVSIGSLLVNFLGEANIAGLAEADAAHYVSYYWGGAM 298

Query: 288 VGRFIGSAAMRYIDDGKALAFNAFVAIILLFITVATTGHIAMWSVLAIGLFNSIMFPTIF 347
           VGRFIGSA MR +  GK LAFNA  A++LL   V   G +AMW+VLA+GLFNSIMFPTIF
Sbjct: 299 VGRFIGSAVMRQVGAGKVLAFNALAAVLLLAAAVLGNGALAMWAVLAVGLFNSIMFPTIF 358

Query: 348 SLALHGLGSHTSQGSGILCLAIVGGAIVPLIQGALADAIGIHLAFLMPIICYAYIAFYGL 407
           SLA+ GLG HT+QGSGILC+AIVGGAIVPL+ G  AD +GI LAF +PI+CY YIAFYGL
Sbjct: 359 SLAVKGLGHHTAQGSGILCMAIVGGAIVPLLVGVAADNLGIQLAFALPILCYLYIAFYGL 418

Query: 408 IGSKS 412
            GS++
Sbjct: 419 KGSQT 423


Lambda     K      H
   0.328    0.141    0.420 

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: 28
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: 412
Length of database: 424
Length adjustment: 32
Effective length of query: 380
Effective length of database: 392
Effective search space:   148960
Effective search space used:   148960
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: 50 (23.9 bits)

This GapMind analysis is from Sep 24 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