GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kgtP in Herbaspirillum seropedicae SmR1

Align Alpha-ketoglutarate permease (characterized)
to candidate HSERO_RS01150 HSERO_RS01150 membrane protein

Query= SwissProt::P0AEX3
         (432 letters)



>FitnessBrowser__HerbieS:HSERO_RS01150
          Length = 433

 Score =  234 bits (596), Expect = 5e-66
 Identities = 142/430 (33%), Positives = 230/430 (53%), Gaps = 23/430 (5%)

Query: 1   MAESTVTADSKLTSSDTRRRIWAIVGASSGNLVEWFDFYVYSFCSLYFAHIFFPSGNTTT 60
           M  ST+ AD  ++ S+ +RR  AIV    GN +EWFDF VYSF ++  A +FFP+GN  T
Sbjct: 1   MQASTLPADGIVSVSNQQRRR-AIVATVIGNGLEWFDFTVYSFFAVIIAKLFFPTGNDLT 59

Query: 61  QLLQTAGVFAAGFLMRPIGGWLFGRIADKHGRKKSMLLSVCMMCFGSLVIACLPGYETIG 120
            LL     F  GF MRP+GG L G  AD+ GRK ++ +++ +M  G+ +I   P YE+IG
Sbjct: 60  SLLLAVATFGVGFFMRPVGGILLGIYADRVGRKAALSVTILLMAVGTTMIGLAPTYESIG 119

Query: 121 TWAPALLLLARLFQGLSVGGEYGTSATYMSEVAVEGRKGFYASFQYVTLIGGQLLALLVV 180
            +AP ++++ARL QG S GGE G++  +++E A E  + +Y+S+   ++    LL   V 
Sbjct: 120 LFAPLIIVVARLLQGFSAGGEMGSATAFLTEYAPERERAYYSSWIQASIGVAVLLGAAVG 179

Query: 181 VVLQHTMEDAALREWGWRIPFALGAVLAVVALWLRRQLDETSQQETRALKEAGSLKGLWR 240
             +  +++ AAL  WGWR+PF LG ++  V  ++R  L+ET        K    LK + R
Sbjct: 180 TFVTASLDAAALASWGWRLPFLLGIIIGPVGYYIRHHLEETPTFLEEKDKTDSPLKEVIR 239

Query: 241 N-----RRAFIMVLGFTAAGSLCFYTFTTYMQKY------LVNTAGMHANVASGIMTAAL 289
           N       +F MV+ +T    +C Y    YM  Y      L  T G  A +  G+     
Sbjct: 240 NFPRETSASFSMVILWT----VCTYVLLFYMPTYSVKVLKLPQTTGFIAGMVGGL----- 290

Query: 290 FVFMLIQPLIGALSDKIGRRTSMLCFGSLAAIFTVPILSALQNVSSPYAAFGLVMCALLI 349
              M++ P++G L+D+IGRR  +    +L  +   P+ + + +  S        +    +
Sbjct: 291 -CIMVLAPIVGRLADRIGRRPLLSGSAALILMLAYPMFAYINSAPSLSTLLIFQLVFGTL 349

Query: 350 VSFYTSISGILKAEMFPAQVRALGVGLSYAVANAIFGGSAE-YVALSLKSIGMETAFFWY 408
           ++ YT       +E+FPA+V + G+ ++Y +A  IFGG A  ++   + + G   A  +Y
Sbjct: 350 IAAYTGPILAAFSELFPAKVLSTGLSVAYNLAVTIFGGFASFFITWLIAATGSTMAPAFY 409

Query: 409 VTLMAVVAFL 418
           V + A ++F+
Sbjct: 410 VMIAAAISFV 419


Lambda     K      H
   0.328    0.138    0.419 

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: 482
Number of extensions: 32
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: 432
Length of database: 433
Length adjustment: 32
Effective length of query: 400
Effective length of database: 401
Effective search space:   160400
Effective search space used:   160400
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 (21.8 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