Alignments for a candidate for HSERO_RS05250 in Rhodobacter johrii JA192

GapMind for catabolism of small carbon sources

Alignments for a candidate for HSERO_RS05250 in Rhodobacter johrii JA192

Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate WP_069330308.1 C8J29_RS17445 sugar ABC transporter ATP-binding protein

Query= uniprot:D8J111
         (520 letters)



>NCBI__GCF_003046325.1:WP_069330308.1
          Length = 497

 Score =  349 bits (896), Expect = e-100
 Identities = 188/490 (38%), Positives = 304/490 (62%), Gaps = 9/490 (1%)

Query: 22  VIALRNVCKRFPGVLALDNCQFELAAGEVHALMGENGAGKSTLMKILSGVYQRDSGDILL 81
           +I LRN+ KRF GV ALD     +  GE+H L GENG+GKST++K++SG+Y  + G+IL+
Sbjct: 5   LIELRNIGKRFGGVRALDGVSLAIRPGEIHCLAGENGSGKSTVIKVMSGIYTPEEGEILI 64

Query: 82  DGKPVEITEPRQAQALGIGIIHQELNLMNHLSAAQNIFIGR---EPRKAMGLFIDEDELN 138
           DG+PV   +P +A   G+ +I+Q+ +L  +L+ A+N+ +     E R+ M    D     
Sbjct: 65  DGRPVGRLDPIRAVQHGVQVIYQDFSLFGNLTVAENLALNTYVLEGRRRM----DWRRAR 120

Query: 139 RQAAAIFARMRLDMDPSTPVGELTVARQQMVEIAKALSFDSRVLIMDEPTAALNNAEIAE 198
             A  + AR+ +D+DP   VG L  + +Q+V IA+A+   +R++IMDEPT AL   E+  
Sbjct: 121 AMAVEVLARIGVDIDPDAEVGTLPTSGRQVVAIARAILARARLIIMDEPTTALTRHEVDA 180

Query: 199 LFRIIRDLQAQGVGIVYISHKMDELRQIADRVSVMRDGKYIATVPMQETSMDTIISMMVG 258
           LF I+RDLQAQG+ ++++SHKM E+ +I++R++V R+G+ +A  PM +     I   M G
Sbjct: 181 LFAIVRDLQAQGIAVLFVSHKMREMLEISERLTVFRNGRKVAEGPMSDFDEAAITHAMTG 240

Query: 259 RALDGEQRIPPDTSRNDVVLEVRGLNRGRAIRDVSFTLRKGEILGFAGLMGAGRTEVARA 318
            +L  +    P       +LEVR L+   +++D+  +LR GEI+G +GL+G+GRTE+ARA
Sbjct: 241 LSLTDDP-YRPALPPGPPLLEVRKLSVPGSVQDIDLSLRPGEIVGISGLIGSGRTELARA 299

Query: 319 IFGADPLEAGEIIIHGGKAVIKSPADAVAHGIGYLSEDRKHFGLAVGMDVQANIALSSMG 378
           +FG +P   G I + G +   +S  +A+A GI Y+ EDR   GL +   ++ N+ +S + 
Sbjct: 300 LFGMEPGMTGTIRLGGREIHPRSVQEAIALGIAYVPEDRLTEGLFLPQSIERNLVVSILE 359

Query: 379 RFTRVGFMDQRAIREAAQMYVRQLAIKTPSVEQQARLLSGGNQQKIVIAKWLLRDCDILF 438
           R  R  F+D RA+RE      R + I  PS E     LSGGN Q++++ +WLL    +L 
Sbjct: 360 RLRRGPFLDTRAVREKTLGMFRDMQIAAPSPETAVGNLSGGNAQRVMLGRWLLTGARVLI 419

Query: 439 FDEPTRGIDVGAKSEIYKLLDALAE-QGKAIVMISSELPEVLRMSHRVLVMCEGRITGEL 497
            + PT G+DVG+K+ I++++  LA+ +G  ++MIS ++PE++   +R+ VM  GR   +L
Sbjct: 420 LNGPTVGVDVGSKATIHRIIRDLAQREGLGVLMISDDVPELVTNCNRIHVMHRGRFVADL 479

Query: 498 ARADATQEKI 507
             +  T+++I
Sbjct: 480 DGSGMTEDRI 489



 Score = 85.1 bits (209), Expect = 5e-21
 Identities = 67/243 (27%), Positives = 115/243 (47%), Gaps = 9/243 (3%)

Query: 274 NDVVLEVRGLNRG----RAIRDVSFTLRKGEILGFAGLMGAGRTEVARAIFGADPLEAGE 329
           +D ++E+R + +     RA+  VS  +R GEI   AG  G+G++ V + + G    E GE
Sbjct: 2   SDTLIELRNIGKRFGGVRALDGVSLAIRPGEIHCLAGENGSGKSTVIKVMSGIYTPEEGE 61

Query: 330 IIIHGGKAVIKSPADAVAHGIGYLSEDRKHFGLAVGMDVQANIALSSMGRFTRVGFMDQR 389
           I+I G       P  AV HG+  + +D   FG    + V  N+AL++     R   MD R
Sbjct: 62  ILIDGRPVGRLDPIRAVQHGVQVIYQDFSLFG---NLTVAENLALNTYVLEGRRR-MDWR 117

Query: 390 AIREAAQMYVRQLAIKTPSVEQQARLLSGGNQQKIVIAKWLLRDCDILFFDEPTRGIDVG 449
             R  A   + ++ +      +   L + G +Q + IA+ +L    ++  DEPT  +   
Sbjct: 118 RARAMAVEVLARIGVDIDPDAEVGTLPTSG-RQVVAIARAILARARLIIMDEPTTALTRH 176

Query: 450 AKSEIYKLLDALAEQGKAIVMISSELPEVLRMSHRVLVMCEGRITGELARADATQEKIMQ 509
               ++ ++  L  QG A++ +S ++ E+L +S R+ V   GR   E   +D  +  I  
Sbjct: 177 EVDALFAIVRDLQAQGIAVLFVSHKMREMLEISERLTVFRNGRKVAEGPMSDFDEAAITH 236

Query: 510 LAT 512
             T
Sbjct: 237 AMT 239


Lambda     K      H
   0.320    0.135    0.372 

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: 601
Number of extensions: 36
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: 520
Length of database: 497
Length adjustment: 34
Effective length of query: 486
Effective length of database: 463
Effective search space:   225018
Effective search space used:   225018
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 (21.8 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