Alignments for a candidate for rbsA in Rhodobacter viridis JA737

GapMind for catabolism of small carbon sources

Alignments for a candidate for rbsA in Rhodobacter viridis JA737

Align ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 (characterized)
to candidate WP_110806166.1 C8J30_RS12430 ABC transporter ATP-binding protein

Query= CharProtDB::CH_003578
         (501 letters)



>NCBI__GCF_003217355.1:WP_110806166.1
          Length = 530

 Score =  292 bits (747), Expect = 2e-83
 Identities = 183/490 (37%), Positives = 281/490 (57%), Gaps = 24/490 (4%)

Query: 5   LQLKGIDKAFPGVKALSGAALNVYPGRVMALVGENGAGKSTMMKVLTGIYTRDAGTLLWL 64
           ++L+GI K+F  V+A    ++ V PG +  +VGENGAGKST+M +L G Y  DAG +L  
Sbjct: 22  IELRGISKSFGAVQANKDISIRVRPGTIHGIVGENGAGKSTLMSILYGFYRADAGEILID 81

Query: 65  GKETTFTGPKSSQEAGIGIIHQELNLIPQLTIAENIFLGREFVNRFGKIDWKTMYAEADK 124
           G+ T     +S+  AGIG++ Q   L+P  ++ EN+ LG E     G +  +   A+A K
Sbjct: 82  GRPTVIPDSQSAIRAGIGMVFQHFKLVPNFSVLENVILGAED----GAL-LRPSLAKARK 136

Query: 125 LLAKL----NLRFKSDKLVGDLSIGDQQMVEIAKVLSFESKVIIMDEPTDALTDTETESL 180
            LA L     L    D LV +LS+G QQ VEI K L   + ++I+DEPT  LT  E + L
Sbjct: 137 TLADLARDYELDVDPDALVEELSVGHQQRVEILKALYRHADILILDEPTGVLTPDEADHL 196

Query: 181 FRVIRELKSQGRGIVYISHRMKEIFEICDDVTVFRDGQFIAEREVASLTEDSLIEMMVGR 240
           FR++R LK+QG+ I+ I+H+++EI EI D+V+V R G+ +A    A  + + L E+MVGR
Sbjct: 197 FRILRGLKAQGKTILLITHKLREIMEITDEVSVMRRGEMVATVTTADTSPEQLAELMVGR 256

Query: 241 KLEDQYPHLDKAPGDIRLKV------DNLCGPGVNDVSFTLRKGEILGVSGLMGAGRTEL 294
           K+    P     PG   L+V      D L    +  ++ T+R GEILG++G+ G G++EL
Sbjct: 257 KVLLHVPKGPANPGREVLRVSDLHVTDALGVERLKGINLTIRAGEILGIAGVAGNGQSEL 316

Query: 295 MKVLYG-ALPRTSGYVTLDGHEVVT----RSPQDGLANGIVYISEDRKRDGLVLGMSVKE 349
           ++VL G A    SG + ++G ++       + Q     GI ++ EDR   GL+L  +  E
Sbjct: 317 LQVLGGFAKGTVSGMIAVEGAQIPAAGKGATGQTRRQIGISHVPEDRHHLGLILDFAAWE 376

Query: 350 NMSL---TALRYFSRAGGSLKHADEQQAVSDFIRLFNVKTPSMEQAIGLLSGGNQQKVAI 406
           N++    +A  Y + A      A  +       R F+V+ P         SGGNQQK+ +
Sbjct: 377 NIAFGYHSAPEYQANALFMDNDAILRDTEGKMDR-FDVRPPDPSLPAKSFSGGNQQKIVL 435

Query: 407 ARGLMTRPKVLILDEPTRGVDVGAKKEIYQLINQFKADGLSIILVSSEMPEVLGMSDRII 466
           AR +   P +L++ +PTRGVD+GA + I++ I + +  G +++LVS E+ E+L +SDRI 
Sbjct: 436 AREIERNPVLLLVGQPTRGVDIGAIEFIHRRIVELRDAGAAVLLVSVELDEILSLSDRIA 495

Query: 467 VMHEGHLSGE 476
           VM +G + GE
Sbjct: 496 VMFDGQIMGE 505



 Score = 95.9 bits (237), Expect = 3e-24
 Identities = 66/227 (29%), Positives = 112/227 (49%), Gaps = 11/227 (4%)

Query: 270 DVSFTLRKGEILGVSGLMGAGRTELMKVLYGALPRTSGYVTLDGHEVVTRSPQDGLANGI 329
           D+S  +R G I G+ G  GAG++ LM +LYG     +G + +DG   V    Q  +  GI
Sbjct: 39  DISIRVRPGTIHGIVGENGAGKSTLMSILYGFYRADAGEILIDGRPTVIPDSQSAIRAGI 98

Query: 330 VYISEDRKRDGLVLGMSVKENMSLTALRYFSRAGGSLKH--ADEQQAVSDFIRLFNVKTP 387
             + +  K   LV   SV EN+ L A       G  L+   A  ++ ++D  R + +   
Sbjct: 99  GMVFQHFK---LVPNFSVLENVILGA-----EDGALLRPSLAKARKTLADLARDYELDVD 150

Query: 388 SMEQAIGLLSGGNQQKVAIARGLMTRPKVLILDEPTRGVDVGAKKEIYQLINQFKADGLS 447
             +  +  LS G+QQ+V I + L     +LILDEPT  +       +++++   KA G +
Sbjct: 151 P-DALVEELSVGHQQRVEILKALYRHADILILDEPTGVLTPDEADHLFRILRGLKAQGKT 209

Query: 448 IILVSSEMPEVLGMSDRIIVMHEGHLSGEFTREQATQEVLMAAAVGK 494
           I+L++ ++ E++ ++D + VM  G +    T    + E L    VG+
Sbjct: 210 ILLITHKLREIMEITDEVSVMRRGEMVATVTTADTSPEQLAELMVGR 256



 Score = 66.2 bits (160), Expect = 3e-15
 Identities = 58/237 (24%), Positives = 103/237 (43%), Gaps = 13/237 (5%)

Query: 16  GVKALSGAALNVYPGRVMALVGENGAGKSTMMKVLTGIYTRD-AGTLLWLGKETTFTGPK 74
           GV+ L G  L +  G ++ + G  G G+S +++VL G      +G +   G +    G  
Sbjct: 286 GVERLKGINLTIRAGEILGIAGVAGNGQSELLQVLGGFAKGTVSGMIAVEGAQIPAAGKG 345

Query: 75  SSQEAG--IGIIH-----QELNLIPQLTIAENIFLGREFVNRFGK----IDWKTMYAEAD 123
           ++ +    IGI H       L LI      ENI  G      +      +D   +  + +
Sbjct: 346 ATGQTRRQIGISHVPEDRHHLGLILDFAAWENIAFGYHSAPEYQANALFMDNDAILRDTE 405

Query: 124 KLLAKLNLRFKSDKLVG-DLSIGDQQMVEIAKVLSFESKVIIMDEPTDALTDTETESLFR 182
             + + ++R     L     S G+QQ + +A+ +     ++++ +PT  +     E + R
Sbjct: 406 GKMDRFDVRPPDPSLPAKSFSGGNQQKIVLAREIERNPVLLLVGQPTRGVDIGAIEFIHR 465

Query: 183 VIRELKSQGRGIVYISHRMKEIFEICDDVTVFRDGQFIAEREVASLTEDSLIEMMVG 239
            I EL+  G  ++ +S  + EI  + D + V  DGQ + ER  A   E  L  +M G
Sbjct: 466 RIVELRDAGAAVLLVSVELDEILSLSDRIAVMFDGQIMGERLPAETNERELGLLMAG 522


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: 613
Number of extensions: 31
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: 530
Length adjustment: 35
Effective length of query: 466
Effective length of database: 495
Effective search space:   230670
Effective search space used:   230670
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 24 2021. The underlying query database was built on Sep 17 2021.

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Protein sequences (fasta format)
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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 2024 update 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