GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|MicrobesOnline__882:206505 DVU1070 branched chain amino acid
           ABC transporter, ATP-binding protein
          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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint 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