GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glcP in Mariniradius saccharolyticus AK6

Align Glucose/fructose:H+ symporter, GlcP (characterized)
to candidate WP_008625717.1 C943_RS06720 sugar porter family MFS transporter

Query= TCDB::P15729
         (468 letters)



>NCBI__GCF_000330725.2:WP_008625717.1
          Length = 469

 Score =  297 bits (761), Expect = 4e-85
 Identities = 175/463 (37%), Positives = 267/463 (57%), Gaps = 20/463 (4%)

Query: 15  KFVLLISGVAALGGFLFGFDTAVINGAVAALQKHFQ-TDSLLTGLSVSLALLGSALGAFG 73
           K++ +IS  AALGGFLFG+D  V+ GA    +  F  T     G   S AL+G  +GA  
Sbjct: 10  KYIWMISLTAALGGFLFGYDWVVVGGAKPFYEPFFNLTSPSEQGWGTSSALVGCMVGAIA 69

Query: 74  AGPIADRHGRIKTMILAAVLFTLSSIGSGLPFTIWDFIFWRVLGGIGVGAASVIAPAYIA 133
              ++D+ GR K +I+A +LF++S+IG+ L  T W F F+R++GGI +G A  ++P YIA
Sbjct: 70  CIFLSDQFGRKKLLIIAGLLFSISAIGTALAPTFWWFNFYRIVGGIAMGIALNLSPLYIA 129

Query: 134 EVSPAHLRGRLGSLQQLAIVSGIFIALLSNWFIALM-------AGGSAQNPWLFGAAAWR 186
           E+SPAH RG L ++ QL I+ G+ +A L NW I+L+       AG         G   WR
Sbjct: 130 EISPAHKRGTLVTINQLLIMIGVLLAQLINWRISLLDIELPEDAGFQMIAASWSGTFGWR 189

Query: 187 WMFWTELIPALLYGVCAFLIPESPRYLVAQGQGEKAAAILWKVEGGD-VPSRIEEIQATV 245
           WMF  E IPA ++ +  F +PESPR+LV   + ++A  IL K+ G     S + EIQ  +
Sbjct: 190 WMFGVEAIPAFVFFLSMFWVPESPRWLVKADRMDEAKKILGKIGGPQYTESALAEIQQNL 249

Query: 246 SLDHKPRFSDLLSRRGGLLPIVWIGMGLSALQQFVGINVIFYYSSVLWRSVGFTEEKSLL 305
           +L+        +  +  +L +V IG+ LS LQQ+ G+NVI YY++ ++++ GF  ++ +L
Sbjct: 250 TLEDPNNSGIGVWLKAPILKVVAIGIFLSFLQQWSGVNVIIYYAADIFQAAGFNLKQMML 309

Query: 306 ITVITGFINILTTLVAIAFVDKFGRKPLLLMGSIGMTITLGILSVVFGGATVVNGQPTLT 365
             V+ G + +L+  + I  VD+FGRK LLL+G+  M I   ++   F             
Sbjct: 310 NIVVIGGVMVLSVFITIYTVDRFGRKVLLLIGTSSMAILYLLIGYSFFAE---------Q 360

Query: 366 GAAGIIALVTANLYVFSFGFSWGPIVWVLLGEMFNNKIRAAALSVAAGVQWIANFIISTT 425
             A ++ LV  N+ V+S  F+  P++WV+L E+F  KIR AA+S+AA   W+ NF ++  
Sbjct: 361 DGASLVVLVLVNVGVYS--FTLAPLLWVVLSEIFPIKIRGAAMSIAALAHWVGNFTLTYF 418

Query: 426 FPPLLDTVGLGPAYGLYATSAAISIFFIWFFVKETKGKTLEQM 468
           FP + + +G    + LY    A   F I F + ETKGK+LEQ+
Sbjct: 419 FPVIKENLGWANNFWLYGAICAFGFFVILFVLPETKGKSLEQI 461


Lambda     K      H
   0.325    0.140    0.430 

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: 618
Number of extensions: 28
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: 468
Length of database: 469
Length adjustment: 33
Effective length of query: 435
Effective length of database: 436
Effective search space:   189660
Effective search space used:   189660
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 51 (24.3 bits)

This GapMind analysis is from Sep 24 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