GapMind for catabolism of small carbon sources

 

Alignments for a candidate for iolT in Bacteroides thetaiotaomicron VPI-5482

Align Major myo-inositol transporter IolT (characterized)
to candidate 353923 BT4397 xylose/H+ symporter (NCBI ptt file)

Query= SwissProt::O34718
         (473 letters)



>FitnessBrowser__Btheta:353923
          Length = 460

 Score =  248 bits (633), Expect = 3e-70
 Identities = 162/464 (34%), Positives = 248/464 (53%), Gaps = 33/464 (7%)

Query: 10  FLRTIILVSTFGGLLFGYDTGVLNGALP----YMGEPDQLNLNAFTEGLVTSSLLFGAAL 65
           F+ +I LVS  GGLLFGYD  V+ GA P    Y G  D   +    +GL  S  L G  +
Sbjct: 8   FVYSICLVSAMGGLLFGYDWVVIGGAKPFYELYFGIADSPTM----QGLAMSVALLGCLI 63

Query: 66  GAVFGGRMSDFNGRRKNILFLAVIFFISTIGCTFAPNVTVMIISRFVLGIAVGGASVTVP 125
           GA+  G M+D  GR+  +L  A IF  S          +  + +RF+ GI +G AS   P
Sbjct: 64  GAMVAGMMADRYGRKPLLLISAFIFLSSAYATGAFSVFSWFLAARFLGGIGIGIASGLSP 123

Query: 126 AYLAEMSPVESRGRMVTQNELMIVSGQLLAFVFNAILGTTMG------------DNSHVW 173
            Y+AE++P   RG++V+ N+L IV G L A + N ++   +             +    W
Sbjct: 124 MYIAEVAPTSIRGKLVSLNQLTIVLGILGAQIANWLIAEPIPADFTPADICASWNGQMGW 183

Query: 174 RFMLVIASLPALFLFFGMIRMPESPRWLVSKGRKEDALRVLKKIRDEKRAAAELQEIE-- 231
           R+M   A+ PA         +PESPRWL  KG++E A  VL +I   + A  ELQ +E  
Sbjct: 184 RWMFWGAAFPAAVFLLLACFIPESPRWLAMKGKREKAWSVLSRIGGNRYAEQELQMVEQT 243

Query: 232 FAFKKEDQLEKATFKDLSVPWVRRIVFIGLGIAIVQQITGVNSIMYYGTEILRNSGFQTE 291
            A K E  L+       S P+ R+++ +G+ +A+ QQ  G N I  Y  EI +++G+   
Sbjct: 244 SASKSEGGLKLL----FSRPF-RKVLVLGVIVAVFQQWCGTNVIFNYAQEIFQSAGYSLG 298

Query: 292 AALIGNIANGVISVLATFVGIWLLGRVGRRPMLMTGLIGTTTALLLIGI-FSLVLEGSPA 350
             L   +  GV +V+ TFV I+ + R+GRR +++ G  G     L++G  +   + G   
Sbjct: 299 DVLFNIVVTGVANVIFTFVAIYTVERLGRRALMLLGAGGLAGIYLVLGTCYFFQVSG--- 355

Query: 351 LPYVVLSLTVTFLAFQQGAISPVTWLMLSEIFPLRLRGLGMGVTVFCLWMVNFAVSFTFP 410
             + ++ L V  +A    ++ P+TW++L+EIFP R+RG+ M    F LW+ +F +++TFP
Sbjct: 356 --FFMVVLVVLAIACYAMSLGPITWVLLAEIFPNRVRGVAMATCTFALWVGSFTLTYTFP 413

Query: 411 ILLAAIGLSTTFFIFVGLGICSVLFVKRFLPETKGLSLEQLEEN 454
           +L  A+G   TF+I+  + +   LF  R LPETKG SLE LE++
Sbjct: 414 LLNTALGSYGTFWIYSAICVFGFLFFLRALPETKGKSLETLEKD 457


Lambda     K      H
   0.327    0.142    0.418 

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: 580
Number of extensions: 31
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: 473
Length of database: 460
Length adjustment: 33
Effective length of query: 440
Effective length of database: 427
Effective search space:   187880
Effective search space used:   187880
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