GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__Btheta:353923 BT4397 xylose/H+ symporter (NCBI
           ptt file)
          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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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