GapMind for catabolism of small carbon sources

 

Alignments 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:

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:

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:

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:

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