GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__Koxy:BWI76_RS14860 BWI76_RS14860 ABC
           transporter
          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 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