GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rbsA in Acidovorax sp. GW101-3H11

Align ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 (characterized)
to candidate Ac3H11_2431 ABC transporter ATP-binding protein

Query= CharProtDB::CH_003578
         (501 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_2431
          Length = 514

 Score =  257 bits (657), Expect = 6e-73
 Identities = 175/520 (33%), Positives = 270/520 (51%), Gaps = 36/520 (6%)

Query: 1   MEALLQLKGIDKAFPGVKALSGAALNVYPGRVMALVGENGAGKSTMMKVLTGIYTRDAGT 60
           M  +L+L  I K F  + A    +L +  G V+AL+GENGAGKST+M +L G Y  D G+
Sbjct: 1   MSNVLRLSHITKRFGKLVANDSISLTLARGEVLALLGENGAGKSTLMSILFGHYVADEGS 60

Query: 61  LLWLGKETTFTGPKSSQEAGIGIIHQELNLIPQLTIAENIFLGREFVNRFGKIDWKTMYA 120
           +   G+      P+++  AGIG++HQ   L   LT+ +N+ LG E +       W+    
Sbjct: 61  IEVFGQPLPPGQPRAALAAGIGMVHQHFTLADNLTVLDNVLLGSEPL-------WQPFSR 113

Query: 121 EAD---KLLA---KLNLRFKSDKLVGDLSIGDQQMVEIAKVLSFESKVIIMDEPTDALTD 174
            ++   KLLA   +  L    D  VG LS+G++Q VEI K L   + ++I+DEPT  LT 
Sbjct: 114 RSEARAKLLAVSQQFGLPVSPDAKVGSLSVGERQRVEILKALYRGAHILILDEPTAVLTP 173

Query: 175 TETESLFRVIRELKSQGRGIVYISHRMKEIFEICDDVTVFRDGQFIAEREVASLTEDSLI 234
            E+E+LF  + ++ +QG  I++ISH++ E+  +   V V R G+ +AE      T+  L 
Sbjct: 174 QESEALFDTLAQMVAQGLSIIFISHKLGEVLRVSHRVAVLRQGKLVAEAPAQGTTQGQLA 233

Query: 235 EMMVGRKLEDQYPHLDKAPGDIRLKVDNL-CGPG----VNDVSFTLRKGEILGVSGLMGA 289
           + MVG  +E       +  G+    + N+   P     +NDVS TLR GEI+ ++G+ G 
Sbjct: 234 QWMVGHAIEAAERRPAQNVGEPICTLSNVSTAPAGRDRLNDVSLTLRAGEIVAIAGVSGN 293

Query: 290 GRTELMKVLYGALPRTSGYVTLDGHEVVTRSPQDGLANGIVYISEDRKRDGLVLGMSVKE 349
           G+  L  VL G    T+G VTL G  +  R P   ++ G+  I EDR   G+V  + V E
Sbjct: 294 GQVALADVLCGVRAATTGQVTLRGAPLQAR-PAWLVSQGVARIPEDRHAVGVVGDLPVWE 352

Query: 350 NMSLTALR--YFS----RAGGSLKHADEQQAVSDFIRLFNVKTPSMEQAIGLLSGGNQQK 403
           N     LR  +F+    RA    + A  Q A       F+V+    +     LSGGN QK
Sbjct: 353 NAVSERLRGPWFAHPWFRAFWVKRRAARQHA-QRVAETFDVRGGGADAPARSLSGGNMQK 411

Query: 404 VAIARGLMTR----------PKVLILDEPTRGVDVGAKKEIYQLINQFKADGLSIILVSS 453
           + + R LM            P++++  +PT G+D+GA   + Q +   +  G +++L+S 
Sbjct: 412 LILGRALMPPQDAAGNSAPVPQLIVAHQPTWGLDIGAVMFVQQQLINARDSGAAVLLISD 471

Query: 454 EMPEVLGMSDRIIVMHEGHLSGEFTREQATQEVLMAAAVG 493
           ++ EVL + DR+ VMH+G LS     E  T+E +  A  G
Sbjct: 472 DLDEVLALGDRVAVMHDGRLSEALPAEGWTREAIGLAMAG 511


Lambda     K      H
   0.318    0.137    0.380 

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: 555
Number of extensions: 23
Number of successful extensions: 9
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: 501
Length of database: 514
Length adjustment: 34
Effective length of query: 467
Effective length of database: 480
Effective search space:   224160
Effective search space used:   224160
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 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