Aligments for a candidate for HSERO_RS05250 in Desulfovibrio vulgaris Hildenborough

GapMind for catabolism of small carbon sources

Aligments for a candidate for HSERO_RS05250 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:D8J111
         (520 letters)



>MicrobesOnline__882:206505
          Length = 524

 Score =  276 bits (706), Expect = 1e-78
 Identities = 172/504 (34%), Positives = 278/504 (55%), Gaps = 18/504 (3%)

Query: 6   ETSTTGVAASSSSSVPVIALRNVCKRFPGVLALDNCQFELAAGEVHALMGENGAGKSTLM 65
           +T  TG A     + PV+ L  + K F  V A  +   ++  G + AL+GENGAGKSTLM
Sbjct: 19  QTGRTGRALRHDVT-PVVRLEGIGKSFGPVRANHDITLDIVPGRIKALLGENGAGKSTLM 77

Query: 66  KILSGVYQRDSGDILLDGKPVEITEPRQAQALGIGIIHQELNLMNHLSAAQNIFIGREPR 125
            ILSG   +D+G I +DG+ V    P+ A   GIG+++Q   L++ ++ A+N+ +G+   
Sbjct: 78  SILSGRLAQDTGIIHVDGEAVRFRSPKDALKAGIGMVYQHFMLVDSMTVAENVLLGQS-- 135

Query: 126 KAMGLFIDEDELNRQAAAIFARMRLDMDPSTPVGELTVARQQMVEIAKALSFDSRVLIMD 185
              G ++    ++R  A + AR  LD+DP+  V +L++  +Q VEI K L  DSRVLI+D
Sbjct: 136 ---GAWLSPVHMSRVVAELAARYGLDIDPAARVCDLSMGERQRVEILKLLYRDSRVLILD 192

Query: 186 EPTAALNNAEIAELFRIIRDLQAQGVGIVYISHKMDELRQIADRVSVMRDGKYIATVPMQ 245
           EPTA L   E  +LF  +  +   G  IV+ISHKM E+  +AD ++++R G+ +      
Sbjct: 193 EPTAVLTPGETEQLFEALHRMAENGKAIVFISHKMQEVLALADEIAILRRGEVVDEFHES 252

Query: 246 ETSMDT-IISMMVGRALDGEQRIPPDTSRNDVVLEVRGLNRGRAIRDVSFTLRKGEILGF 304
           E   +  + + MVGR +  E    P     D VL V GL  G  ++ +SF +RKGE+   
Sbjct: 253 EVPGEAELANRMVGREVILEVAAEP-LEPGDRVLHVDGL-AGDGLKGLSFEVRKGEVFAI 310

Query: 305 AGLMGAGRTEVARAIFGADPLEAGEIIIHG---GKAVIKSPADAVAHGIGYLSEDRKHFG 361
           AG+ G G+ E+   + G      GE+ + G    +   K+P      G+ Y+ EDR+   
Sbjct: 311 AGVAGNGQRELVECVTGLRRPAEGEVELLGIPWRQFFTKAPRQG---GLAYIPEDRQGLA 367

Query: 362 LAVGMDVQANIALSSMGRFTRVGFMDQRAIREAAQMYVRQLAIKTPSVEQQARLLSGGNQ 421
             + +D+  N  L++ G FTR  F+D+++   AA+  + +  ++    E  AR LSGGN 
Sbjct: 368 TCLSLDLVDNFLLTARGCFTRGPFLDRKSADAAARDILAEYNVQPGRAEAPARSLSGGNL 427

Query: 422 QKIVIAKWLLRDCDILFFDEPTRGIDVGAKSEIY-KLLDALAEQGKAIVMISSELPEVLR 480
           QK+V+ +   R   ++  + PT+G+D+ A  E++ +LL+  +  G  ++++S +L EVL 
Sbjct: 428 QKLVVGREFYRKPSLIVAENPTQGLDIAATEEVWARLLEVRSHAG--VLLVSGDLNEVLA 485

Query: 481 MSHRVLVMCEGRITGELARADATQ 504
           ++ RV VM  G   G L R+D  +
Sbjct: 486 LADRVAVMYRGCFIGLLDRSDTNK 509



 Score = 96.3 bits (238), Expect = 2e-24
 Identities = 71/241 (29%), Positives = 115/241 (47%), Gaps = 19/241 (7%)

Query: 273 RNDV--VLEVRGLNRG----RAIRDVSFTLRKGEILGFAGLMGAGRTEVARAIFGADPLE 326
           R+DV  V+ + G+ +     RA  D++  +  G I    G  GAG++ +   + G    +
Sbjct: 28  RHDVTPVVRLEGIGKSFGPVRANHDITLDIVPGRIKALLGENGAGKSTLMSILSGRLAQD 87

Query: 327 AGEIIIHGGKAVIKSPADAVAHGIGYLSEDRKHFGLAVGMDVQANIALSSMGRFTRVGFM 386
            G I + G     +SP DA+  GIG + +   HF L   M V  N+ L   G +     M
Sbjct: 88  TGIIHVDGEAVRFRSPKDALKAGIGMVYQ---HFMLVDSMTVAENVLLGQSGAWLSPVHM 144

Query: 387 DQRAIREAAQMYVRQLAIKTPSVEQQARL--LSGGNQQKIVIAKWLLRDCDILFFDEPTR 444
             R + E A  Y          ++  AR+  LS G +Q++ I K L RD  +L  DEPT 
Sbjct: 145 S-RVVAELAARYGLD-------IDPAARVCDLSMGERQRVEILKLLYRDSRVLILDEPTA 196

Query: 445 GIDVGAKSEIYKLLDALAEQGKAIVMISSELPEVLRMSHRVLVMCEGRITGELARADATQ 504
            +  G   ++++ L  +AE GKAIV IS ++ EVL ++  + ++  G +  E   ++   
Sbjct: 197 VLTPGETEQLFEALHRMAENGKAIVFISHKMQEVLALADEIAILRRGEVVDEFHESEVPG 256

Query: 505 E 505
           E
Sbjct: 257 E 257


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: 647
Number of extensions: 35
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: 524
Length adjustment: 35
Effective length of query: 485
Effective length of database: 489
Effective search space:   237165
Effective search space used:   237165
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, or view the source code.

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