Alignments for a candidate for HSERO_RS05250 in Rhodobacter viridis JA737

GapMind for catabolism of small carbon sources

Alignments for a candidate for HSERO_RS05250 in Rhodobacter viridis JA737

Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate WP_110805317.1 C8J30_RS07980 ABC transporter ATP-binding protein

Query= uniprot:D8J111
         (520 letters)



>NCBI__GCF_003217355.1:WP_110805317.1
          Length = 505

 Score =  293 bits (750), Expect = 1e-83
 Identities = 175/497 (35%), Positives = 275/497 (55%), Gaps = 22/497 (4%)

Query: 22  VIALRNVCKRFPGVLALDNCQFELAAGEVHALMGENGAGKSTLMKILSGVYQRDSGDILL 81
           ++ +  + K +PGV+A D   FE+A GEVHAL+GENGAGKSTL+K++ G+ + D+G +  
Sbjct: 5   LLKIEGLTKAYPGVVANDGVGFEVAPGEVHALLGENGAGKSTLVKMIYGLVKPDAGRMTF 64

Query: 82  DGKPVEITEPRQAQALGIGIIHQELNLMNHLSAAQNIFIGREPRKAMGLFIDEDELNRQA 141
            G+P    EPR A+A G+ ++ Q  +L   L+ A+N+ +G E    MG      +L  + 
Sbjct: 65  QGRPYTPAEPRAARAAGVAMVFQHFSLFEALNVAENVALGMENPPPMG------DLAERI 118

Query: 142 AAIFARMRLDMDPSTPVGELTVARQQMVEIAKALSFDSRVLIMDEPTAALNNAEIAELFR 201
            AI     L +DP+  VG+L+   +Q VEI + L  D ++LIMDEPT+ L   E+  LF 
Sbjct: 119 RAISTAYGLPLDPARTVGDLSAGERQRVEIIRCLLQDPKLLIMDEPTSVLTPQEVEILFH 178

Query: 202 IIRDLQAQGVGIVYISHKMDELRQIADRVSVMRDGKYIATVPMQETSMDTIISMMVG--- 258
            +R L A+G  I+YISHK++E+R + D  +++R GK +A+   +E S   +  +MVG   
Sbjct: 179 TLRKLAAEGTAILYISHKLEEIRSLCDGATILRGGKVVASCIPREKSARELAELMVGGEF 238

Query: 259 RALDGEQRIPPDTSRNDVVLEVRGLNR------GRAIRDVSFTLRKGEILGFAGLMGAGR 312
            A D   R+   T     +LEV  LN       G A+++VSF+L  GE+LG  G+ G G+
Sbjct: 239 AATDRAGRVSGAT-----ILEVDHLNLPPMTQFGPALKNVSFSLAAGEVLGIGGVAGNGQ 293

Query: 313 TEVARAIFGADPLEAGEIIIHGGKAVIKSPADAVAHGIGYLSEDRKHFGLAVGMDVQANI 372
            E+   + G  P  AG + +HG       P D    G+    E+R        + +  N 
Sbjct: 294 EELLATLSGERPSGAGTVSLHGQDISDLGPNDRRRLGLLAAPEERLGHAAVPNLSLTENA 353

Query: 373 ALSSMGR--FTRVGFMDQRAIREAAQMYVRQLAIKTPSVEQQARLLSGGNQQKIVIAKWL 430
            L+   R   TR GF++  A R  A+  ++   ++TP     AR LSGGN QK VI + +
Sbjct: 354 ILTGTVRRPLTRNGFLNMGAARRFAEEIIKGFDVRTPGPHVAARALSGGNLQKFVIGREV 413

Query: 431 LRDCDILFFDEPTRGIDVGAKSEIYKLLDALAEQGKAIVMISSELPEVLRMSHRVLVMCE 490
           L+  ++L  ++PT G+D  A + I + L  LA +G A+++IS +L E++ ++ R   + E
Sbjct: 414 LQSPEVLVVNQPTWGVDAAAAAAIRQSLLDLAAKGAAVIVISQDLDELMEIADRFCALNE 473

Query: 491 GRITGELARADATQEKI 507
           GR++        T E+I
Sbjct: 474 GRLSEPRPTEGLTMEEI 490



 Score = 78.2 bits (191), Expect = 7e-19
 Identities = 67/232 (28%), Positives = 107/232 (46%), Gaps = 14/232 (6%)

Query: 37  ALDNCQFELAAGEVHALMGENGAGKSTLMKILSGVYQRDSGDILLDGKPVEITEPRQAQA 96
           AL N  F LAAGEV  + G  G G+  L+  LSG     +G + L G+ +    P   + 
Sbjct: 269 ALKNVSFSLAAGEVLGIGGVAGNGQEELLATLSGERPSGAGTVSLHGQDISDLGPNDRRR 328

Query: 97  LGIGIIHQEL---NLMNHLSAAQNIFIGREPRKAMGLFIDEDELNRQAAAIFARMRLD-M 152
           LG+    +E      + +LS  +N  +    R+ +        LN  AA  FA   +   
Sbjct: 329 LGLLAAPEERLGHAAVPNLSLTENAILTGTVRRPL---TRNGFLNMGAARRFAEEIIKGF 385

Query: 153 DPSTPVGELTVARQ------QMVEIAKALSFDSRVLIMDEPTAALNNAEIAELFRIIRDL 206
           D  TP G    AR       Q   I + +     VL++++PT  ++ A  A + + + DL
Sbjct: 386 DVRTP-GPHVAARALSGGNLQKFVIGREVLQSPEVLVVNQPTWGVDAAAAAAIRQSLLDL 444

Query: 207 QAQGVGIVYISHKMDELRQIADRVSVMRDGKYIATVPMQETSMDTIISMMVG 258
            A+G  ++ IS  +DEL +IADR   + +G+     P +  +M+ I  M+ G
Sbjct: 445 AAKGAAVIVISQDLDELMEIADRFCALNEGRLSEPRPTEGLTMEEIGLMLGG 496



 Score = 70.9 bits (172), Expect = 1e-16
 Identities = 63/245 (25%), Positives = 110/245 (44%), Gaps = 14/245 (5%)

Query: 277 VLEVRGLNR---GRAIRD-VSFTLRKGEILGFAGLMGAGRTEVARAIFGADPLEAGEIII 332
           +L++ GL +   G    D V F +  GE+    G  GAG++ + + I+G    +AG +  
Sbjct: 5   LLKIEGLTKAYPGVVANDGVGFEVAPGEVHALLGENGAGKSTLVKMIYGLVKPDAGRMTF 64

Query: 333 HGGKAVIKSPADAVAHGIGYLSEDRKHFGLAVGMDVQANIALSSMGRFTRVGFMDQRAIR 392
            G       P  A A G+  + +   HF L   ++V  N+AL  M     +G + +R IR
Sbjct: 65  QGRPYTPAEPRAARAAGVAMVFQ---HFSLFEALNVAENVALG-MENPPPMGDLAER-IR 119

Query: 393 EAAQMYVRQLAIKTPSVEQQARLLSGGNQQKIVIAKWLLRDCDILFFDEPTRGIDVGAKS 452
             +  Y   L        +    LS G +Q++ I + LL+D  +L  DEPT  +      
Sbjct: 120 AISTAYGLPL-----DPARTVGDLSAGERQRVEIIRCLLQDPKLLIMDEPTSVLTPQEVE 174

Query: 453 EIYKLLDALAEQGKAIVMISSELPEVLRMSHRVLVMCEGRITGELARADATQEKIMQLAT 512
            ++  L  LA +G AI+ IS +L E+  +     ++  G++       + +  ++ +L  
Sbjct: 175 ILFHTLRKLAAEGTAILYISHKLEEIRSLCDGATILRGGKVVASCIPREKSARELAELMV 234

Query: 513 QRESA 517
             E A
Sbjct: 235 GGEFA 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: 585
Number of extensions: 31
Number of successful extensions: 8
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: 520
Length of database: 505
Length adjustment: 35
Effective length of query: 485
Effective length of database: 470
Effective search space:   227950
Effective search space used:   227950
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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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
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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