GapMind for catabolism of small carbon sources

 

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

Align D-fructose transporter, sugar porter family (characterized)
to candidate Echvi_2810 Echvi_2810 MFS transporter, sugar porter (SP) family

Query= reanno::Korea:Ga0059261_1777
         (458 letters)



>FitnessBrowser__Cola:Echvi_2810
          Length = 450

 Score =  317 bits (813), Expect = 4e-91
 Identities = 181/427 (42%), Positives = 269/427 (62%), Gaps = 10/427 (2%)

Query: 30  ALGGLLFGFDTAVISGATQALQLQFGLTDAMLGFTVAS-ALIGTVLGSLIAGAPADRFGR 88
           +L G LFGFDTAVISGA   L+  +  +D   GF + S AL GTV+G+L+ G P    GR
Sbjct: 13  SLTGFLFGFDTAVISGANLPLKALWQTSDWFHGFFIMSVALWGTVIGALLGGIPCHHLGR 72

Query: 89  KGVMLTVAIAYVVSSLGTGLAPDLNAFLVFRFMGGLAIGAASVVTPIYIAEVSPARFRGR 148
           K  +  + + ++VS+LGT LA D   F  +RF+GG+AIGA+S+  P Y++E+S A  RGR
Sbjct: 73  KNTLFWIGVMFLVSALGTALATDPFVFSFYRFVGGVAIGASSIAAPTYVSEISQAYQRGR 132

Query: 149 LVAMNQLNIVLGILIAFLSNYIIAGLVQYDVAWRWMFGIVAVPSTIFLLVTLLLPESPRW 208
            V + Q+NIV GIL+A++SNY++ G+  ++  WRWM     +P+ I+L   L +PESPRW
Sbjct: 133 RVGLYQINIVSGILVAYVSNYLLQGVGDHN-DWRWMLAAEIIPAIIYLAFILDIPESPRW 191

Query: 209 LAIHGQAD-RARDVMQRLGFADPRAELARIELAEAREEAAGKPRLFQRSHFTPVACAIAI 267
           L +  + +  A+ V++++        L  I+    R +   K +LF   +  P+  A  I
Sbjct: 192 LILKQKDESAAQKVLKKITTGKIDQLLLSIKHDSLRSK---KMKLFSAKNRLPLFLAGII 248

Query: 268 AMFNQLSGINALLYYAPRIFELAGAGADSALLQSIAVGGTNLVFTVAALFLIDRFGRRPL 327
           A+FNQLSGIN +LYYAP I E AG    ++LL ++ +G TNL+FT+  + LID+ GR+ L
Sbjct: 249 AIFNQLSGINFILYYAPEIMEKAGFVTTTSLLGAVCIGFTNLIFTLIGMSLIDKTGRKQL 308

Query: 328 LFVGSVICAATLLLVGWQL-ESAKPDGTLILFGLLGFIAAFAMSQGAVIWVFISEVFPSA 386
           + +GS+    +L LV +   +S+ P    IL  +L FIAA  + QGAVIWVFISE+FP+ 
Sbjct: 309 MLIGSMGYIISLGLVSYGFYDSSSP--LFILTSILIFIAAHGIGQGAVIWVFISEIFPNK 366

Query: 387 VRGKGQALGSTTHWVMAAAITWAFPVFAASVGGW-VFAFFGAMMLLQLLWTWKFMPETNG 445
           VR  GQ+ G+  HW  AA IT    V   ++  + +F  F A+M+LQ ++ W++MPET G
Sbjct: 367 VRAMGQSFGAGVHWGGAAMITLFGAVLIDTLMPFQIFMVFMALMILQFVFVWRYMPETKG 426

Query: 446 IALEDMN 452
           + LE+++
Sbjct: 427 LELENLH 433


Lambda     K      H
   0.327    0.139    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: 576
Number of extensions: 27
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: 458
Length of database: 450
Length adjustment: 33
Effective length of query: 425
Effective length of database: 417
Effective search space:   177225
Effective search space used:   177225
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.

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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