Alignments for a candidate for HSERO_RS03640 in Rhodobacter viridis JA737

GapMind for catabolism of small carbon sources

Alignments for a candidate for HSERO_RS03640 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:D8IZC7
         (521 letters)



>NCBI__GCF_003217355.1:WP_110805317.1
          Length = 505

 Score =  283 bits (724), Expect = 1e-80
 Identities = 169/495 (34%), Positives = 267/495 (53%), Gaps = 16/495 (3%)

Query: 6   LLQMRGIRKSFGATLALSDMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQGEILL 65
           LL++ G+ K++   +A   +   + PGE+HAL+GENGAGKSTL+K++ G+  PD G +  
Sbjct: 5   LLKIEGLTKAYPGVVANDGVGFEVAPGEVHALLGENGAGKSTLVKMIYGLVKPDAGRMTF 64

Query: 66  DGRPVALRDPGASRAAGINLIYQELAVAPNISVAANVFMGSELRTRLGLIDHAAMRSRTD 125
            GRP    +P A+RAAG+ +++Q  ++   ++VA NV +G E    +G      +  R  
Sbjct: 65  QGRPYTPAEPRAARAAGVAMVFQHFSLFEALNVAENVALGMENPPPMG-----DLAERIR 119

Query: 126 AVLRQLGAGFGASDLAGRLSIAEQQQVEIARALVHRSRIVIMDEPTAALSERETEQLFNV 185
           A+    G     +   G LS  E+Q+VEI R L+   +++IMDEPT+ L+ +E E LF+ 
Sbjct: 120 AISTAYGLPLDPARTVGDLSAGERQRVEIIRCLLQDPKLLIMDEPTSVLTPQEVEILFHT 179

Query: 186 VRRLRDEGLAIIYISHRMAEVYALADRVTVLRDGSFVGELVRDEIDSERIVQMMVGRSLS 245
           +R+L  EG AI+YISH++ E+ +L D  T+LR G  V   +  E  +  + ++MVG   +
Sbjct: 180 LRKLAAEGTAILYISHKLEEIRSLCDGATILRGGKVVASCIPREKSARELAELMVGGEFA 239

Query: 246 EFYQHQRIAPA-----DAAQLPTVMQVRALAGGKIRPASFDVRAGEVLGFAGLVGAGRTE 300
              +  R++ A     D   LP + Q     G  ++  SF + AGEVLG  G+ G G+ E
Sbjct: 240 ATDRAGRVSGATILEVDHLNLPPMTQF----GPALKNVSFSLAAGEVLGIGGVAGNGQEE 295

Query: 301 LARLLFGADPRSGGDILLEGRPVHIDQPRAAMRAGIAYVPEDRKGQGLFLQMAVAANATM 360
           L   L G  P   G + L G+ +    P    R G+   PE+R G      +++  NA +
Sbjct: 296 LLATLSGERPSGAGTVSLHGQDISDLGPNDRRRLGLLAAPEERLGHAAVPNLSLTENAIL 355

Query: 361 NVASRH--TRLGLVRSRSLGGVARAAIQRLNVKVAHPETPVGKLSGGNQQKVLLARWLEI 418
               R   TR G +   +    A   I+  +V+   P      LSGGN QK ++ R +  
Sbjct: 356 TGTVRRPLTRNGFLNMGAARRFAEEIIKGFDVRTPGPHVAARALSGGNLQKFVIGREVLQ 415

Query: 419 APKVLILDEPTRGVDIYAKSEIYQLVHRLASQGVAVVVISSELPEVIGICDRVLVMREGM 478
           +P+VL++++PT GVD  A + I Q +  LA++G AV+VIS +L E++ I DR   + EG 
Sbjct: 416 SPEVLVVNQPTWGVDAAAAAAIRQSLLDLAAKGAAVIVISQDLDELMEIADRFCALNEGR 475

Query: 479 ITGELAGAAITQENI 493
           ++       +T E I
Sbjct: 476 LSEPRPTEGLTMEEI 490



 Score = 69.3 bits (168), Expect = 3e-16
 Identities = 54/228 (23%), Positives = 100/228 (43%), Gaps = 7/228 (3%)

Query: 21  ALSDMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQGEILLDGRPVALRDPGASRA 80
           AL ++  ++  GE+  + G  G G+  L+  LSG      G + L G+ ++   P   R 
Sbjct: 269 ALKNVSFSLAAGEVLGIGGVAGNGQEELLATLSGERPSGAGTVSLHGQDISDLGPNDRRR 328

Query: 81  AGINLIYQEL---AVAPNISVAANVFMGSELR---TRLGLIDHAAMRSRTDAVLRQLGAG 134
            G+    +E    A  PN+S+  N  +   +R   TR G ++  A R   + +++     
Sbjct: 329 LGLLAAPEERLGHAAVPNLSLTENAILTGTVRRPLTRNGFLNMGAARRFAEEIIKGFDVR 388

Query: 135 FGASDLAGR-LSIAEQQQVEIARALVHRSRIVIMDEPTAALSERETEQLFNVVRRLRDEG 193
                +A R LS    Q+  I R ++    ++++++PT  +       +   +  L  +G
Sbjct: 389 TPGPHVAARALSGGNLQKFVIGREVLQSPEVLVVNQPTWGVDAAAAAAIRQSLLDLAAKG 448

Query: 194 LAIIYISHRMAEVYALADRVTVLRDGSFVGELVRDEIDSERIVQMMVG 241
            A+I IS  + E+  +ADR   L +G        + +  E I  M+ G
Sbjct: 449 AAVIVISQDLDELMEIADRFCALNEGRLSEPRPTEGLTMEEIGLMLGG 496


Lambda     K      H
   0.320    0.135    0.378 

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: 676
Number of extensions: 37
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: 521
Length of database: 505
Length adjustment: 35
Effective length of query: 486
Effective length of database: 470
Effective search space:   228420
Effective search space used:   228420
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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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