GapMind for catabolism of small carbon sources

 

Alignments for a candidate for araG in Klebsiella michiganensis M5al

Align L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 (characterized)
to candidate BWI76_RS14860 BWI76_RS14860 ABC transporter

Query= CharProtDB::CH_014279
         (504 letters)



>FitnessBrowser__Koxy:BWI76_RS14860
          Length = 510

 Score =  389 bits (999), Expect = e-112
 Identities = 217/493 (44%), Positives = 315/493 (63%), Gaps = 10/493 (2%)

Query: 4   STPYLSFRGIGKTFPGVKALTDISFDCYAGQVHALMGENGAGKSTLLKILSGNYAPTTGS 63
           S P L   GI K +    AL ++ FD +AG+VHALMGENGAGKSTL+KILSGN    +G 
Sbjct: 6   SPPLLRLEGISKRYGATLALNNVRFDLFAGEVHALMGENGAGKSTLMKILSGNEQRDSGV 65

Query: 64  VVINGQEMSFSDTTAALNAGVAIIYQELHLVPEMTVAENIYLGQLPHK-GGIVNRSLLNY 122
           + I+GQ +       A   G+AII+QEL+ VP+MTVAEN++LGQ P    GI++R  ++ 
Sbjct: 66  IFIDGQAIDIRTPRDARKYGIAIIHQELNTVPDMTVAENLFLGQEPTSFAGILDRKRMHR 125

Query: 123 EAGLQLKHLGMDIDPDTPLKYLSIGQWQMVEIAKALARNAKIIAFDEPTSSLSAREIDNL 182
           EA  +L  +  DIDP  PL  LSIG+ QMVEIA+A++ NAK++  DEPT++LS  E   L
Sbjct: 126 EAKEKLNRINADIDPQAPLGSLSIGRQQMVEIARAVSENAKVLVLDEPTAALSRAETLQL 185

Query: 183 FRVIRELRKEGRVILYVSHRMEEIFALSDAITVFKDGRYVKTFTDMQQVDHDALVQAMVG 242
           +R+I ++R++G  ++Y+SHRMEE++ L++ +TVF+DG ++ T  ++  V    +V+ MVG
Sbjct: 186 YRLIAQMRQDGVGMVYISHRMEEVWQLANRVTVFRDGTWIGT-ENLGNVSTTDIVRMMVG 244

Query: 243 RDIGDIYGWQPRSYGEERLRLDAVKAPGVRTPISLAVRSGEIVGLFGLVGAGRSELMKGM 302
           R I D+Y  +PR+ G+  L +  + A     P+S  V +GE+V + GLVG+GR+E+ + +
Sbjct: 245 RQIVDLYQHEPRTPGDVLLEVRDL-AGSATGPVSFEVSAGEVVSMSGLVGSGRTEVARLL 303

Query: 303 FGGTQITAGQVYI---DQQPIDIRKPSHAIAAGMMLCPEDRKAEGIIPVHSVRDNINISA 359
           FG    + G V +   + QP D   P+ AIA G+ +  EDRK +G+   HSV  NI+IS+
Sbjct: 304 FGADPRSQGSVRLAGRESQPSD---PTAAIADGIGMVTEDRKTQGLFLGHSVEHNIDISS 360

Query: 360 RRKHVLGGCVINNGWEENNADHHIRSLNIKTPGAEQLIMNLSGGNQQKAILGRWLSEEMK 419
               V GG V+            +R L ++    E  +  LSGGNQQKA L RWL  + +
Sbjct: 361 LDNFVAGG-VVKRKTIRAAVLEQMRRLRLRENAVELPVSALSGGNQQKAALARWLLRDSR 419

Query: 420 VILLDEPTRGIDVGAKHEIYNVIYALAAQGVAVLFASSDLPEVLGVADRIVVMREGEIAG 479
           +++LDEPTRG+D+GAK EIY +I  LA  G A+L  SSDLPE +G++DR++VMR G I  
Sbjct: 420 LLILDEPTRGVDIGAKREIYELIDRLARAGKAILVISSDLPEAIGISDRVLVMRGGRIVH 479

Query: 480 ELLHEQADERQAL 492
           +L    A E + +
Sbjct: 480 QLPSCSATEEEVM 492



 Score = 88.6 bits (218), Expect = 5e-22
 Identities = 58/220 (26%), Positives = 111/220 (50%), Gaps = 6/220 (2%)

Query: 26  ISFDCYAGQVHALMGENGAGKSTLLKILSGNYAPTTGSVVINGQEMSFSDTTAALNAGVA 85
           +SF+  AG+V ++ G  G+G++ + ++L G    + GSV + G+E   SD TAA+  G+ 
Sbjct: 276 VSFEVSAGEVVSMSGLVGSGRTEVARLLFGADPRSQGSVRLAGRESQPSDPTAAIADGIG 335

Query: 86  IIYQELH---LVPEMTVAENIYLGQLPH--KGGIVNRSLLNYEAGLQLKHLGMDIDP-DT 139
           ++ ++     L    +V  NI +  L +   GG+V R  +      Q++ L +  +  + 
Sbjct: 336 MVTEDRKTQGLFLGHSVEHNIDISSLDNFVAGGVVKRKTIRAAVLEQMRRLRLRENAVEL 395

Query: 140 PLKYLSIGQWQMVEIAKALARNAKIIAFDEPTSSLSAREIDNLFRVIRELRKEGRVILYV 199
           P+  LS G  Q   +A+ L R+++++  DEPT  +       ++ +I  L + G+ IL +
Sbjct: 396 PVSALSGGNQQKAALARWLLRDSRLLILDEPTRGVDIGAKREIYELIDRLARAGKAILVI 455

Query: 200 SHRMEEIFALSDAITVFKDGRYVKTFTDMQQVDHDALVQA 239
           S  + E   +SD + V + GR V         + + ++ A
Sbjct: 456 SSDLPEAIGISDRVLVMRGGRIVHQLPSCSATEEEVMLHA 495


Lambda     K      H
   0.319    0.136    0.391 

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: 689
Number of extensions: 35
Number of successful extensions: 9
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 504
Length of database: 510
Length adjustment: 34
Effective length of query: 470
Effective length of database: 476
Effective search space:   223720
Effective search space used:   223720
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 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