GapMind for catabolism of small carbon sources

 

Alignments for a candidate for BPHYT_RS34245 in Desulfovibrio vulgaris Hildenborough

Align ABC transporter related; Flags: Precursor (characterized, see rationale)
to candidate 206505 DVU1070 branched chain amino acid ABC transporter, ATP-binding protein

Query= uniprot:B2T9V9
         (510 letters)



>MicrobesOnline__882:206505
          Length = 524

 Score =  222 bits (565), Expect = 3e-62
 Identities = 148/473 (31%), Positives = 234/473 (49%), Gaps = 11/473 (2%)

Query: 13  PVVEALEVTKRFGSTAALNDVSIRVMPGESHALVGRNGAGKSTLVSILTGLRKPDTGEVR 72
           PVV    + K FG   A +D+++ ++PG   AL+G NGAGKSTL+SIL+G    DTG + 
Sbjct: 33  PVVRLEGIGKSFGPVRANHDITLDIVPGRIKALLGENGAGKSTLMSILSGRLAQDTGIIH 92

Query: 73  FSGAAAPSIADRDAWRERVACVYQHSTIIRDLSVAENLFINRQPLRGGVIDWQAMRRDAR 132
             G A    + +DA +  +  VYQH  ++  ++VAEN+ + +    G  +    M R   
Sbjct: 93  VDGEAVRFRSPKDALKAGIGMVYQHFMLVDSMTVAENVLLGQS---GAWLSPVHMSRVVA 149

Query: 133 ALLDHWKIDVREDARAGDLSVEARQLVEIARALSYGARFIILDEPTAQLDGDEIKRLFRR 192
            L   + +D+   AR  DLS+  RQ VEI + L   +R +ILDEPTA L   E ++LF  
Sbjct: 150 ELAARYGLDIDPAARVCDLSMGERQRVEILKLLYRDSRVLILDEPTAVLTPGETEQLFEA 209

Query: 193 ISELQREGVTFLFISHHLQEVYEICQAVTVLRDARHIVSAPVSALPRE-QLIEAMTGERG 251
           +  +   G   +FISH +QEV  +   + +LR    +     S +P E +L   M G   
Sbjct: 210 LHRMAENGKAIVFISHKMQEVLALADEIAILRRGEVVDEFHESEVPGEAELANRMVGRE- 268

Query: 252 GLAVADAAARGALPADTAVALELKELTGADYEGVSFTVKRGEVVGLTGATSSGRTSVAEA 311
              + + AA    P D    L +  L G   +G+SF V++GEV  + G   +G+  + E 
Sbjct: 269 --VILEVAAEPLEPGDR--VLHVDGLAGDGLKGLSFEVRKGEVFAIAGVAGNGQRELVEC 324

Query: 312 IAGLRAAKRGTISVDGAILPPGDVPASLAHGIGCVPKDRHHEGLVLTQSVAENASMTIAR 371
           + GLR    G + + G         A    G+  +P+DR      L+  + +N  +T   
Sbjct: 325 VTGLRRPAEGEVELLGIPWRQFFTKAPRQGGLAYIPEDRQGLATCLSLDLVDNFLLTARG 384

Query: 372 VLGKFGIAAPAKKNAFGQKMIDALGIVAQGPEHVVSGLSGGNQQKVVMARALATNPNVLV 431
              +         +A  + ++    +     E     LSGGN QK+V+ R     P+++V
Sbjct: 385 CFTRGPFLDRKSADAAARDILAEYNVQPGRAEAPARSLSGGNLQKLVVGREFYRKPSLIV 444

Query: 432 LIDPTAGVDVKSKEALLSVVDRVREEGKAVLVVSGELDD-LRTCDRVLVMFRG 483
             +PT G+D+ + E + + +  VR     VL+VSG+L++ L   DRV VM+RG
Sbjct: 445 AENPTQGLDIAATEEVWARLLEVRSHA-GVLLVSGDLNEVLALADRVAVMYRG 496


Lambda     K      H
   0.318    0.134    0.377 

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: 652
Number of extensions: 30
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 510
Length of database: 524
Length adjustment: 35
Effective length of query: 475
Effective length of database: 489
Effective search space:   232275
Effective search space used:   232275
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 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