Alignments for a candidate for rbsA in Azospirillum brasilense Sp245

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_RS06625 AZOBR_RS06625 heme ABC transporter ATP-binding protein

Query= CharProtDB::CH_003578
         (501 letters)



>FitnessBrowser__azobra:AZOBR_RS06625
          Length = 511

 Score =  286 bits (731), Expect = 2e-81
 Identities = 179/501 (35%), Positives = 277/501 (55%), Gaps = 26/501 (5%)

Query: 5   LQLKGIDKAFPGVKALSGAALNVYPGRVMALVGENGAGKSTMMKVLTGIYTRDAGTLLWL 64
           L+ +G++K F    A    +L V  G +  ++GENGAGKST+M ++ G    D GT+L  
Sbjct: 8   LETRGVNKWFGANHANRDVSLAVPKGTIHGVIGENGAGKSTIMSIVYGYLPADGGTILVD 67

Query: 65  GKETTFTGPKSSQEAGIGIIHQELNLIPQLTIAENIFLGREFVNRFGKIDWKTMYAEADK 124
           G+      P+ +  AGIG++HQ   L+   T+ EN+ LG E     G +      A A  
Sbjct: 68  GRPVAVRSPRDALAAGIGMVHQHFMLVDPFTVLENVLLGAE-----GGVTLAAGMARART 122

Query: 125 LLAKL----NLRFKSDKLVGDLSIGDQQMVEIAKVLSFESKVIIMDEPTDALTDTETESL 180
            L +L     L    D+ VG+L +G QQ VEI K L   + ++I+DEPT  LT  ET+ L
Sbjct: 123 ELTRLARDYGLEVDLDRPVGELPVGAQQRVEILKALYRGADILILDEPTGVLTPQETDHL 182

Query: 181 FRVIRELKSQGRGIVYISHRMKEIFEICDDVTVFRDGQFIAEREVASLTEDSLIEMMVGR 240
           FR++R L+ QG+ +V I+H+++EI E+ D+VTV R GQ +A    A  + + L E+MVGR
Sbjct: 183 FRILRALREQGKTVVIITHKLREIMELTDNVTVMRRGQVVANVATARTSREELAELMVGR 242

Query: 241 KLEDQYPHLDKAPGDIRLKVDNLC---GPG---VNDVSFTLRKGEILGVSGLMGAGRTEL 294
           K+  +   +   PG   L+V  LC   G G   V  +  T+R GEI+G++G+ G G++EL
Sbjct: 243 KVLLRVEKVPATPGPAVLEVSGLCVRDGAGVERVKGIGLTVRAGEIVGIAGVSGNGQSEL 302

Query: 295 MKVLYGALPRTSGYVTLDGHEVVT---RSPQDGL-ANGIVYISEDRKRDGLVLGMSVKEN 350
           ++ L G  P   G V L G E+     R    GL A G+ ++ EDR+R GLV G   +E 
Sbjct: 303 LEALAGMRPPAEGSVRLRGEELTATPDRFTARGLRALGVGHVPEDRQRVGLVTGFEAQE- 361

Query: 351 MSLTALRYFSRAGGSLKHADEQQAVSD----FIRLFNVKTPSMEQAIGLLSGGNQQKVAI 406
                L +      + +   +++A+ D     +  ++V+           SGGNQQK+ +
Sbjct: 362 --CAILGHQGDPAFNGRLLMDRRALFDRCASEMDAYDVRPRDPRLPAANFSGGNQQKIVL 419

Query: 407 ARGLMTRPKVLILDEPTRGVDVGAKKEIYQLINQFKADGLSIILVSSEMPEVLGMSDRII 466
           AR +   P +L++ +PTRGVD+GA + I++ +   +  G +I+LVS E+ E+  +SDRI+
Sbjct: 420 AREMERNPDLLLVGQPTRGVDIGAIEFIHRRLVALRDQGKAILLVSVELDEIRALSDRIL 479

Query: 467 VMHEGHLSGEFTREQATQEVL 487
           VM +G L GE    +A +  L
Sbjct: 480 VMFDGRLVGEVAPGEADERRL 500



 Score =  103 bits (258), Expect = 1e-26
 Identities = 65/225 (28%), Positives = 117/225 (52%), Gaps = 7/225 (3%)

Query: 270 DVSFTLRKGEILGVSGLMGAGRTELMKVLYGALPRTSGYVTLDGHEVVTRSPQDGLANGI 329
           DVS  + KG I GV G  GAG++ +M ++YG LP   G + +DG  V  RSP+D LA GI
Sbjct: 25  DVSLAVPKGTIHGVIGENGAGKSTIMSIVYGYLPADGGTILVDGRPVAVRSPRDALAAGI 84

Query: 330 VYISEDRKRDGLVLGMSVKENMSLTALRYFSRAGGSLKHADEQQAVSDFIRLFNVKTPSM 389
             + +      LV   +V EN+ L A    + A G  +   E   ++   R + ++   +
Sbjct: 85  GMVHQHFM---LVDPFTVLENVLLGAEGGVTLAAGMARARTE---LTRLARDYGLEV-DL 137

Query: 390 EQAIGLLSGGNQQKVAIARGLMTRPKVLILDEPTRGVDVGAKKEIYQLINQFKADGLSII 449
           ++ +G L  G QQ+V I + L     +LILDEPT  +       +++++   +  G +++
Sbjct: 138 DRPVGELPVGAQQRVEILKALYRGADILILDEPTGVLTPQETDHLFRILRALREQGKTVV 197

Query: 450 LVSSEMPEVLGMSDRIIVMHEGHLSGEFTREQATQEVLMAAAVGK 494
           +++ ++ E++ ++D + VM  G +       + ++E L    VG+
Sbjct: 198 IITHKLREIMELTDNVTVMRRGQVVANVATARTSREELAELMVGR 242



 Score = 70.1 bits (170), Expect = 2e-16
 Identities = 57/249 (22%), Positives = 115/249 (46%), Gaps = 12/249 (4%)

Query: 3   ALLQLKGID-KAFPGVKALSGAALNVYPGRVMALVGENGAGKSTMMKVLTGIYTRDAGTL 61
           A+L++ G+  +   GV+ + G  L V  G ++ + G +G G+S +++ L G+     G++
Sbjct: 258 AVLEVSGLCVRDGAGVERVKGIGLTVRAGEIVGIAGVSGNGQSELLEALAGMRPPAEGSV 317

Query: 62  LWLGKETTFTGPKSSQEA----GIGII---HQELNLIPQLTIAENIFLGREFVNRFGK-- 112
              G+E T T  + +       G+G +    Q + L+      E   LG +    F    
Sbjct: 318 RLRGEELTATPDRFTARGLRALGVGHVPEDRQRVGLVTGFEAQECAILGHQGDPAFNGRL 377

Query: 113 -IDWKTMYAEADKLLAKLNLRFKSDKL-VGDLSIGDQQMVEIAKVLSFESKVIIMDEPTD 170
            +D + ++      +   ++R +  +L   + S G+QQ + +A+ +     ++++ +PT 
Sbjct: 378 LMDRRALFDRCASEMDAYDVRPRDPRLPAANFSGGNQQKIVLAREMERNPDLLLVGQPTR 437

Query: 171 ALTDTETESLFRVIRELKSQGRGIVYISHRMKEIFEICDDVTVFRDGQFIAEREVASLTE 230
            +     E + R +  L+ QG+ I+ +S  + EI  + D + V  DG+ + E       E
Sbjct: 438 GVDIGAIEFIHRRLVALRDQGKAILLVSVELDEIRALSDRILVMFDGRLVGEVAPGEADE 497

Query: 231 DSLIEMMVG 239
             L  MM G
Sbjct: 498 RRLGLMMAG 506


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: 634
Number of extensions: 30
Number of successful extensions: 9
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 3
Length of query: 501
Length of database: 511
Length adjustment: 34
Effective length of query: 467
Effective length of database: 477
Effective search space:   222759
Effective search space used:   222759
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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources