Alignments for a candidate for HSERO_RS03640 in Desulfovibrio vulgaris Miyazaki F

GapMind for catabolism of small carbon sources

Alignments for a candidate for HSERO_RS03640 in Desulfovibrio vulgaris Miyazaki F

Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate 8502321 DvMF_3029 ABC transporter related (RefSeq)

Query= uniprot:D8IZC7
         (521 letters)



>FitnessBrowser__Miya:8502321
          Length = 537

 Score =  275 bits (704), Expect = 2e-78
 Identities = 165/476 (34%), Positives = 264/476 (55%), Gaps = 14/476 (2%)

Query: 5   PLLQMRGIRKSFGATLALSDMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQGEIL 64
           P++++ GI KSFG   A  D+ L IRPG I AL+GENGAGKSTLM +L+G    D G I+
Sbjct: 28  PVVRLDGICKSFGKVRANHDITLDIRPGCIKALLGENGAGKSTLMSILAGKLRQDAGTIV 87

Query: 65  LDGRPVALRDPGASRAAGINLIYQELAVAPNISVAANVFMGSELRTRLGLIDHAAMRSRT 124
           +DG P     P  +  AGI ++YQ   +  +++VA NV +G        L+  A MR   
Sbjct: 88  VDGVPTVFASPRDALRAGIGMVYQHFMLVDSMTVAENVLLGQSPDM---LLRPARMRDEV 144

Query: 125 DAVLRQLGAGFGASDLAGRLSIAEQQQVEIARALVHRSRIVIMDEPTAALSERETEQLFN 184
            A+  + G     +   G LS+ E+Q+VEI + L   SR++I+DEPTA L+ RET+QLF 
Sbjct: 145 AALAERYGLAVDPAARVGGLSMGERQRVEILKLLYRDSRVLILDEPTAVLTPRETDQLFE 204

Query: 185 VVRRLRDEGLAIIYISHRMAEVYALADRVTVLRDGSFVGELVRDEIDSERIV-QMMVGRS 243
            + R+ D+G A+++ISH++ EV  +AD + +LR G  V E    ++ ++ ++   MVGR 
Sbjct: 205 AMWRMADQGKALVFISHKLQEVLTVADEIAILRRGEVVDEFSEADVPNQTVLANRMVGRD 264

Query: 244 LSEFYQHQRIAPADAAQLPTVMQVRALAGGKIRPASFDVRAGEVLGFAGLVGAGRTELAR 303
           +      +R+ P D     TV+ V  L+G  +   S  VR GE++  AG+ G G+ EL  
Sbjct: 265 VVLQVDAKRLTPVD-----TVLSVEHLSGAGLSDVSLQVRRGEIVAIAGVAGNGQKELVE 319

Query: 304 LLFGADPRSGGDILLEGRPVHIDQPRAAMRAGIAYVPEDRKGQGLFLQMAVAANATMNVA 363
            + G      G++ + GRP          R G+AY+PEDR+G      + +  N  +   
Sbjct: 320 AICGLARPEAGEVRILGRPWREFFAGPPGRRGLAYIPEDRQGLATCRHLDLVDNFLLTTR 379

Query: 364 SRHTR-LGLVRSRSLGGVARAAIQRLNVKVAHPETPVGKLSGGNQQKVLLARWLEIAPKV 422
           ++  + + L R+ +   V R  +   NV+      P   LSGGN QK+++ R     P+V
Sbjct: 380 NQFAKGVFLDRTEATNAVKR-VVWEYNVQPGDITAPARALSGGNLQKLVIGREFFRKPEV 438

Query: 423 LILDEPTRGVDIYAKSEIY-QLVHRLASQGVAVVVISSELPEVIGICDRVLVMREG 477
           ++ + PT+G+DI A  E++ +L+   ++ G  V++++ +L E + + DR+ VM  G
Sbjct: 439 IVAENPTQGLDISATEEVWGRLLEARSTSG--VLLVTGDLNEALELADRIAVMYRG 492



 Score = 97.1 bits (240), Expect = 1e-24
 Identities = 72/241 (29%), Positives = 120/241 (49%), Gaps = 13/241 (5%)

Query: 259 AQLPTVMQVRALAG--GKIRP---ASFDVRAGEVLGFAGLVGAGRTELARLLFGADPRSG 313
           A LP V+++  +    GK+R     + D+R G +    G  GAG++ L  +L G   +  
Sbjct: 24  AHLPPVVRLDGICKSFGKVRANHDITLDIRPGCIKALLGENGAGKSTLMSILAGKLRQDA 83

Query: 314 GDILLEGRPVHIDQPRAAMRAGIAYVPEDRKGQGLFLQMAVAANATMNVASRHTRLGLVR 373
           G I+++G P     PR A+RAGI  V +      L   M VA N  +  +       L+R
Sbjct: 84  GTIVVDGVPTVFASPRDALRAGIGMVYQHFM---LVDSMTVAENVLLGQSPDM----LLR 136

Query: 374 SRSLGGVARAAIQRLNVKVAHPETPVGKLSGGNQQKVLLARWLEIAPKVLILDEPTRGVD 433
              +     A  +R  + V  P   VG LS G +Q+V + + L    +VLILDEPT  + 
Sbjct: 137 PARMRDEVAALAERYGLAV-DPAARVGGLSMGERQRVEILKLLYRDSRVLILDEPTAVLT 195

Query: 434 IYAKSEIYQLVHRLASQGVAVVVISSELPEVIGICDRVLVMREGMITGELAGAAITQENI 493
                ++++ + R+A QG A+V IS +L EV+ + D + ++R G +  E + A +  + +
Sbjct: 196 PRETDQLFEAMWRMADQGKALVFISHKLQEVLTVADEIAILRRGEVVDEFSEADVPNQTV 255

Query: 494 M 494
           +
Sbjct: 256 L 256



 Score = 69.7 bits (169), Expect = 3e-16
 Identities = 58/242 (23%), Positives = 108/242 (44%), Gaps = 8/242 (3%)

Query: 4   TPLLQMRGIRKSFGATLALSDMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQGEI 63
           TP+  +  +    GA   LSD+ L +R GEI A+ G  G G+  L++ + G+  P+ GE+
Sbjct: 275 TPVDTVLSVEHLSGA--GLSDVSLQVRRGEIVAIAGVAGNGQKELVEAICGLARPEAGEV 332

Query: 64  LLDGRP---VALRDPGASRAAGINLIYQELAVAPNISVAANVFMGSELRTRLGL-IDHAA 119
            + GRP        PG    A I    Q LA   ++ +  N  + +  +   G+ +D   
Sbjct: 333 RILGRPWREFFAGPPGRRGLAYIPEDRQGLATCRHLDLVDNFLLTTRNQFAKGVFLDRTE 392

Query: 120 MRSRTDAVLRQLGAGFGASDLAGR-LSIAEQQQVEIARALVHRSRIVIMDEPTAALSERE 178
             +    V+ +     G      R LS    Q++ I R    +  +++ + PT  L    
Sbjct: 393 ATNAVKRVVWEYNVQPGDITAPARALSGGNLQKLVIGREFFRKPEVIVAENPTQGLDISA 452

Query: 179 TEQLFNVVRRLRDEGLAIIYISHRMAEVYALADRVTVLRDGSFVGELVRDEIDSERIVQM 238
           TE+++  +   R     ++ ++  + E   LADR+ V+  G F+    +D+    + + +
Sbjct: 453 TEEVWGRLLEARSTS-GVLLVTGDLNEALELADRIAVMYRGRFIDVFDKDDTAKVQAIGL 511

Query: 239 MV 240
           M+
Sbjct: 512 MM 513


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: 731
Number of extensions: 44
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: 537
Length adjustment: 35
Effective length of query: 486
Effective length of database: 502
Effective search space:   243972
Effective search space used:   243972
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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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