GapMind for catabolism of small carbon sources

 

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

Align Probable inositol transporter 2 (characterized)
to candidate 353132 BT3606 sugar-proton symporter (NCBI ptt file)

Query= SwissProt::Q9C757
         (580 letters)



>FitnessBrowser__Btheta:353132
          Length = 468

 Score =  200 bits (508), Expect = 1e-55
 Identities = 161/550 (29%), Positives = 260/550 (47%), Gaps = 111/550 (20%)

Query: 27  YVLRLAFSAGIGGLLFGYDTGVISGALLYIRDDFKSVDRNTWLQEMIVSMAVAGAIVGAA 86
           Y++ L+  A +GG LFGYDT VISG +  +   F+    +T  Q   V  A+ G+IVG  
Sbjct: 9   YIIFLSVVAALGGFLFGYDTAVISGTIAQVTHLFQL---DTLQQGWYVGCALIGSIVGVL 65

Query: 87  IGGWANDKLGRRSAILMADFLFLLGAIIMAAAPNPSLLVVGRVFVGLGVGMASMTAPLYI 146
             G  +D +GR+  ++++  LF   AI  A   + + LVV R+  G+G+G+ S+ +PLYI
Sbjct: 66  FSGILSDSIGRKRTMILSAILFSTSAIGCAFCIDFNQLVVYRIIGGIGIGVVSIVSPLYI 125

Query: 147 SEASPAKIRGALVSTNGFLITGGQFLSYLIN---LAFTD--------------VTGTWRW 189
           SE S A+ RG +VS     +T G   +YL+N   LA+++              VT  WR 
Sbjct: 126 SEVSVAQFRGRMVSLYQLAVTVGFLGAYLVNYQLLAYSESGNHLPIAWLEKIVVTEVWRG 185

Query: 190 MLGIAGIPALLQFVLMFTLPESPRWLYRKGREEEAKAILRRIY-SAEDVEQEIRALKDSV 248
           MLG+  +PA++ F+++F +PESPRWL  KG+E +A  IL +IY S ++ + ++   K  +
Sbjct: 186 MLGMETLPAIIFFIIIFFIPESPRWLIVKGQERKATYILEKIYNSFKEADFQLNETKSVL 245

Query: 249 ETEILEEGSSEKINMIKLCKAKTVRRGLIAGVGLQVFQQFVGINTVMYYSPTIVQLAGFA 308
            +E   E S        +     + + +I GV + +  QF+G+N V+YY P+I + AG  
Sbjct: 246 VSETRSEWS--------ILLKPGILKAVIIGVCIAILGQFMGVNAVLYYGPSIFENAGL- 296

Query: 309 SNRTALLLSLVTAGLNAFGSIISIYFIDRIGRKKLLIISLFGVIISLGILTGVFYEAATH 368
           S   +L   ++   +N   +I+++  ID++GRKKL+   + G+++SL IL G ++     
Sbjct: 297 SGGDSLFYQVLVGLVNTLTTILALLIIDKVGRKKLIYYGVSGMVVSL-ILIGSYF----- 350

Query: 369 APAISSLETQRFNNISCPDYKSAMNTNAWDCMTCLKASSPSCGYCSSPIGKEHPGACWIS 428
                                  +  NAW+  +    +   C          +   C IS
Sbjct: 351 -----------------------LFGNAWNISSLFLLAFFLC----------YVFCCAIS 377

Query: 429 DDSVKDLCHNENRLWYTRGCPSNFGWFALLGLGLYIIFFSPGMGTVPWIVNSEIYPLRFR 488
             +V  +  +E      RG   +   FA L +G Y+I    G  T PW+           
Sbjct: 378 ICAVIFVLLSEMYPTKIRGLAMSIAGFA-LWIGTYLI----GQLT-PWM----------- 420

Query: 489 GICGGIAATANWISNLIVAQSFLSLTEAIGTSWTFLIFGVISVIALLFVMVCVPETKGMP 548
                       + NL  A +F              +F ++ V  +L V   VPET G  
Sbjct: 421 ------------LQNLTPAGTF-------------FLFAIMCVPYMLIVWKLVPETTGKS 455

Query: 549 MEEIEKMLER 558
           +EEIE+   R
Sbjct: 456 LEEIERYWTR 465


Lambda     K      H
   0.324    0.139    0.425 

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: 713
Number of extensions: 39
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 3
Length of query: 580
Length of database: 468
Length adjustment: 35
Effective length of query: 545
Effective length of database: 433
Effective search space:   235985
Effective search space used:   235985
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 (21.5 bits)
S2: 52 (24.6 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