Alignments for a candidate for HSERO_RS03640 in Desulfovibrio vulgaris Hildenborough

GapMind for catabolism of small carbon sources

Alignments for a candidate for HSERO_RS03640 in Desulfovibrio vulgaris Hildenborough

Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate 206505 DVU1070 branched chain amino acid ABC transporter, ATP-binding protein

Query= uniprot:D8IZC7
         (521 letters)



>MicrobesOnline__882:206505
          Length = 524

 Score =  290 bits (741), Expect = 1e-82
 Identities = 183/485 (37%), Positives = 264/485 (54%), Gaps = 19/485 (3%)

Query: 4   TPLLQMRGIRKSFGATLALSDMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQGEI 63
           TP++++ GI KSFG   A  D+ L I PG I AL+GENGAGKSTLM +LSG  A D G I
Sbjct: 32  TPVVRLEGIGKSFGPVRANHDITLDIVPGRIKALLGENGAGKSTLMSILSGRLAQDTGII 91

Query: 64  LLDGRPVALRDPGASRAAGINLIYQELAVAPNISVAANVFMGSELRTRLGLIDHAAMRSR 123
            +DG  V  R P  +  AGI ++YQ   +  +++VA NV +G       G        SR
Sbjct: 92  HVDGEAVRFRSPKDALKAGIGMVYQHFMLVDSMTVAENVLLGQS-----GAWLSPVHMSR 146

Query: 124 TDAVLRQLGAGFGAS-DLAGR---LSIAEQQQVEIARALVHRSRIVIMDEPTAALSERET 179
              V+ +L A +G   D A R   LS+ E+Q+VEI + L   SR++I+DEPTA L+  ET
Sbjct: 147 ---VVAELAARYGLDIDPAARVCDLSMGERQRVEILKLLYRDSRVLILDEPTAVLTPGET 203

Query: 180 EQLFNVVRRLRDEGLAIIYISHRMAEVYALADRVTVLRDGSFVGELVRDEIDSE-RIVQM 238
           EQLF  + R+ + G AI++ISH+M EV ALAD + +LR G  V E    E+  E  +   
Sbjct: 204 EQLFEALHRMAENGKAIVFISHKMQEVLALADEIAILRRGEVVDEFHESEVPGEAELANR 263

Query: 239 MVGRSLSEFYQHQRIAPADAAQLPTVMQVRALAGGKIRPASFDVRAGEVLGFAGLVGAGR 298
           MVGR +      + + P D      V+ V  LAG  ++  SF+VR GEV   AG+ G G+
Sbjct: 264 MVGREVILEVAAEPLEPGDR-----VLHVDGLAGDGLKGLSFEVRKGEVFAIAGVAGNGQ 318

Query: 299 TELARLLFGADPRSGGDILLEGRPVHIDQPRAAMRAGIAYVPEDRKGQGLFLQMAVAANA 358
            EL   + G    + G++ L G P      +A  + G+AY+PEDR+G    L + +  N 
Sbjct: 319 RELVECVTGLRRPAEGEVELLGIPWRQFFTKAPRQGGLAYIPEDRQGLATCLSLDLVDNF 378

Query: 359 TMNVASRHTRLGLVRSRSLGGVARAAIQRLNVKVAHPETPVGKLSGGNQQKVLLARWLEI 418
            +      TR   +  +S    AR  +   NV+    E P   LSGGN QK+++ R    
Sbjct: 379 LLTARGCFTRGPFLDRKSADAAARDILAEYNVQPGRAEAPARSLSGGNLQKLVVGREFYR 438

Query: 419 APKVLILDEPTRGVDIYAKSEIYQLVHRLASQGVAVVVISSELPEVIGICDRVLVMREGM 478
            P +++ + PT+G+DI A  E++  +  + S    V+++S +L EV+ + DRV VM  G 
Sbjct: 439 KPSLIVAENPTQGLDIAATEEVWARLLEVRSH-AGVLLVSGDLNEVLALADRVAVMYRGC 497

Query: 479 ITGEL 483
             G L
Sbjct: 498 FIGLL 502



 Score = 79.3 bits (194), Expect = 3e-19
 Identities = 62/236 (26%), Positives = 107/236 (45%), Gaps = 20/236 (8%)

Query: 279 SFDVRAGEVLGFAGLVGAGRTELARLLFGADPRSGGDILLEGRPVHIDQPRAAMRAGIAY 338
           + D+  G +    G  GAG++ L  +L G   +  G I ++G  V    P+ A++AGI  
Sbjct: 54  TLDIVPGRIKALLGENGAGKSTLMSILSGRLAQDTGIIHVDGEAVRFRSPKDALKAGIGM 113

Query: 339 VPEDRKGQGLFLQMAVAANATMNVASRHTRLGLVRSRSLGGVARAAIQRLNVKVAHPETP 398
           V +      L   M VA N  +  +        +    +  V      R  + +  P   
Sbjct: 114 VYQHFM---LVDSMTVAENVLLGQSG-----AWLSPVHMSRVVAELAARYGLDI-DPAAR 164

Query: 399 VGKLSGGNQQKVLLARWLEIAPKVLILDEPTRGVDIYAKSEIYQLVHRLASQGVAVVVIS 458
           V  LS G +Q+V + + L    +VLILDEPT  +      ++++ +HR+A  G A+V IS
Sbjct: 165 VCDLSMGERQRVEILKLLYRDSRVLILDEPTAVLTPGETEQLFEALHRMAENGKAIVFIS 224

Query: 459 SELPEVIGICDRVLVMREGMIT-----------GELAGAAITQENIMRLATDTNVP 503
            ++ EV+ + D + ++R G +             ELA   + +E I+ +A +   P
Sbjct: 225 HKMQEVLALADEIAILRRGEVVDEFHESEVPGEAELANRMVGREVILEVAAEPLEP 280



 Score = 73.2 bits (178), Expect = 2e-17
 Identities = 59/228 (25%), Positives = 108/228 (47%), Gaps = 7/228 (3%)

Query: 22  LSDMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQGEILLDGRPVALRDPGASRAA 81
           L  +   +R GE+ A+ G  G G+  L++ ++G+  P +GE+ L G P       A R  
Sbjct: 295 LKGLSFEVRKGEVFAIAGVAGNGQRELVECVTGLRRPAEGEVELLGIPWRQFFTKAPRQG 354

Query: 82  GINLIYQE---LAVAPNISVAANVFMGSE-LRTRLGLIDHAAMRSRTDAVLRQLGAGFGA 137
           G+  I ++   LA   ++ +  N  + +    TR   +D  +  +    +L +     G 
Sbjct: 355 GLAYIPEDRQGLATCLSLDLVDNFLLTARGCFTRGPFLDRKSADAAARDILAEYNVQPGR 414

Query: 138 SDLAGR-LSIAEQQQVEIARALVHRSRIVIMDEPTAALSERETEQLFNVVRRLRDEGLAI 196
           ++   R LS    Q++ + R    +  +++ + PT  L    TE+++  +  +R     +
Sbjct: 415 AEAPARSLSGGNLQKLVVGREFYRKPSLIVAENPTQGLDIAATEEVWARLLEVRSHA-GV 473

Query: 197 IYISHRMAEVYALADRVTVLRDGSFVGELVRDEIDS-ERIVQMMVGRS 243
           + +S  + EV ALADRV V+  G F+G L R + +  + I  MM G S
Sbjct: 474 LLVSGDLNEVLALADRVAVMYRGCFIGLLDRSDTNKVDAIGLMMAGVS 521


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: 697
Number of extensions: 48
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: 521
Length of database: 524
Length adjustment: 35
Effective length of query: 486
Effective length of database: 489
Effective search space:   237654
Effective search space used:   237654
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 17 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 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