GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rbsA in Azospirillum brasilense Sp245

Align ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 (characterized)
to candidate AZOBR_RS31880 AZOBR_RS31880 sugar ABC transporter ATP-binding protein

Query= CharProtDB::CH_003578
         (501 letters)



>FitnessBrowser__azobra:AZOBR_RS31880
          Length = 515

 Score =  286 bits (732), Expect = 1e-81
 Identities = 168/480 (35%), Positives = 270/480 (56%), Gaps = 13/480 (2%)

Query: 4   LLQLKGIDKAFPGVKALSGAALNVYPGRVMALVGENGAGKSTMMKVLTGIYTRDAGTLLW 63
           +L+L GI K F  + A    +L ++ G V+AL+GENGAGK+T+M +L G Y  D G++  
Sbjct: 7   VLRLSGITKRFGPLVANDSISLTLHKGEVLALLGENGAGKTTLMNILFGHYVADEGSIEA 66

Query: 64  LGKETTFTGPKSSQEAGIGIIHQELNLIPQLTIAENIFLGREFVNRFGKIDWKTMYAEAD 123
            G+      P+++  AGIG++HQ   L   L++ +NI +G E + R  + D     A+  
Sbjct: 67  FGQPLPPGSPRAALAAGIGMVHQHFTLADNLSVLDNIAVGTESLWR-PRSDRAAAKAKLL 125

Query: 124 KLLAKLNLRFKSDKLVGDLSIGDQQMVEIAKVLSFESKVIIMDEPTDALTDTETESLFRV 183
            L  +  L  + D LVGDLS+G++Q  EI K L  +++V+I+DEPT  LT  E+ SLF  
Sbjct: 126 DLARRFGLEVRPDALVGDLSVGERQRAEILKALYRDARVLILDEPTAVLTPQESASLFDT 185

Query: 184 IRELKSQGRGIVYISHRMKEIFEICDDVTVFRDGQFIAEREVASLTEDSLIEMMVGRKLE 243
           +R L + G  +V+ISH+M E+F   D V V R G+ +A R+ A    + L E+MVGR L+
Sbjct: 186 LRRLTADGLAVVFISHKMNEVFAASDTVAVLRGGRLVATRKTAETDREELAELMVGRALK 245

Query: 244 DQYPHLDKAPGDIRLKVDNLC------GPGVNDVSFTLRKGEILGVSGLMGAGRTELMKV 297
              P     PG+  L +  +        P ++ V  T+R+ +I+G++G+ G G+T L ++
Sbjct: 246 PPTP-TPLEPGEPVLTLSGVTVASGHGRPLLDGVDLTVRRRQIVGIAGVSGNGQTALAEL 304

Query: 298 LYGALPRTSGYVTLDGHEVVTRSPQDGLANGIVYISEDRKRDGLVLGMSVKENMSLTALR 357
           + G +   SG +TL G  +    P + +  G+  I EDR   GLV  M+V EN  L A R
Sbjct: 305 ISGLIHPDSGTMTLKGEAIGNAEPAEMVRRGVARIPEDRHAAGLVGAMAVWEN--LIAER 362

Query: 358 YFSRA---GGSLKHADEQQAVSDFIRLFNVKTPSMEQAIGLLSGGNQQKVAIARGLMTRP 414
           Y   A    G ++    +    + I  F+V+ P  +    LLSGGN QK+ + R L   P
Sbjct: 363 YHDPAFQRFGLIRRGAARAYAEEVIAAFDVRCPGPDARTQLLSGGNMQKLILGRTLAHGP 422

Query: 415 KVLILDEPTRGVDVGAKKEIYQLINQFKADGLSIILVSSEMPEVLGMSDRIIVMHEGHLS 474
            +++  +PTRG+DVGA   ++  + + +A G  ++++S ++ E+L ++D I V + G L+
Sbjct: 423 DLILASQPTRGLDVGAVSYVHGRLLEARAAGAGVLVISEDLDEILALADGITVAYHGRLT 482



 Score = 92.0 bits (227), Expect = 4e-23
 Identities = 66/227 (29%), Positives = 110/227 (48%), Gaps = 9/227 (3%)

Query: 269 NDVSFTLRKGEILGVSGLMGAGRTELMKVLYGALPRTSGYVTLDGHEVVTRSPQDGLANG 328
           + +S TL KGE+L + G  GAG+T LM +L+G      G +   G  +   SP+  LA G
Sbjct: 24  DSISLTLHKGEVLALLGENGAGKTTLMNILFGHYVADEGSIEAFGQPLPPGSPRAALAAG 83

Query: 329 IVYISEDRKRDGLVLGMSVKENMSL-TALRYFSRAGGSLKHADEQQAVSDFIRLFNVKTP 387
           I  + +      L   +SV +N+++ T   +  R+      A  +  + D  R F ++  
Sbjct: 84  IGMVHQHFT---LADNLSVLDNIAVGTESLWRPRSD----RAAAKAKLLDLARRFGLEVR 136

Query: 388 SMEQAIGLLSGGNQQKVAIARGLMTRPKVLILDEPTRGVDVGAKKEIYQLINQFKADGLS 447
             +  +G LS G +Q+  I + L    +VLILDEPT  +       ++  + +  ADGL+
Sbjct: 137 P-DALVGDLSVGERQRAEILKALYRDARVLILDEPTAVLTPQESASLFDTLRRLTADGLA 195

Query: 448 IILVSSEMPEVLGMSDRIIVMHEGHLSGEFTREQATQEVLMAAAVGK 494
           ++ +S +M EV   SD + V+  G L       +  +E L    VG+
Sbjct: 196 VVFISHKMNEVFAASDTVAVLRGGRLVATRKTAETDREELAELMVGR 242


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: 633
Number of extensions: 29
Number of successful extensions: 7
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: 501
Length of database: 515
Length adjustment: 34
Effective length of query: 467
Effective length of database: 481
Effective search space:   224627
Effective search space used:   224627
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