GapMind for catabolism of small carbon sources

 

Alignments for a candidate for BPHYT_RS34245 in Desulfovibrio vulgaris Miyazaki F

Align ABC transporter related; Flags: Precursor (characterized, see rationale)
to candidate 8502321 DvMF_3029 ABC transporter related (RefSeq)

Query= uniprot:B2T9V9
         (510 letters)



>FitnessBrowser__Miya:8502321
          Length = 537

 Score =  219 bits (557), Expect = 3e-61
 Identities = 156/503 (31%), Positives = 241/503 (47%), Gaps = 27/503 (5%)

Query: 13  PVVEALEVTKRFGSTAALNDVSIRVMPGESHALVGRNGAGKSTLVSILTGLRKPDTGEVR 72
           PVV    + K FG   A +D+++ + PG   AL+G NGAGKSTL+SIL G  + D G + 
Sbjct: 28  PVVRLDGICKSFGKVRANHDITLDIRPGCIKALLGENGAGKSTLMSILAGKLRQDAGTIV 87

Query: 73  FSGAAAPSIADRDAWRERVACVYQHSTIIRDLSVAENLFINRQPLRGGVIDWQAMRRDAR 132
             G      + RDA R  +  VYQH  ++  ++VAEN+ + + P    ++    MR +  
Sbjct: 88  VDGVPTVFASPRDALRAGIGMVYQHFMLVDSMTVAENVLLGQSP--DMLLRPARMRDEVA 145

Query: 133 ALLDHWKIDVREDARAGDLSVEARQLVEIARALSYGARFIILDEPTAQLDGDEIKRLFRR 192
           AL + + + V   AR G LS+  RQ VEI + L   +R +ILDEPTA L   E  +LF  
Sbjct: 146 ALAERYGLAVDPAARVGGLSMGERQRVEILKLLYRDSRVLILDEPTAVLTPRETDQLFEA 205

Query: 193 ISELQREGVTFLFISHHLQEVYEICQAVTVLRDARHIVSAPVSALPREQ-LIEAMTGERG 251
           +  +  +G   +FISH LQEV  +   + +LR    +     + +P +  L   M G   
Sbjct: 206 MWRMADQGKALVFISHKLQEVLTVADEIAILRRGEVVDEFSEADVPNQTVLANRMVGRD- 264

Query: 252 GLAVADAAARGALPADTAVALELKELTGADYEGVSFTVKRGEVVGLTGATSSGRTSVAEA 311
              V    A+   P DT +++E   L+GA    VS  V+RGE+V + G   +G+  + EA
Sbjct: 265 --VVLQVDAKRLTPVDTVLSVE--HLSGAGLSDVSLQVRRGEIVAIAGVAGNGQKELVEA 320

Query: 312 IAGLRAAKRGTISVDGA------ILPPGDVPASLAHGIGCVPKDRHHEGLVLTQSVAENA 365
           I GL   + G + + G         PPG        G+  +P+DR          + +N 
Sbjct: 321 ICGLARPEAGEVRILGRPWREFFAGPPG------RRGLAYIPEDRQGLATCRHLDLVDNF 374

Query: 366 SMTIARVLGKFGIAAPAKKNAFGQKMIDALGIVAQGPEHVVSGLSGGNQQKVVMARALAT 425
            +T      K       +     ++++    +           LSGGN QK+V+ R    
Sbjct: 375 LLTTRNQFAKGVFLDRTEATNAVKRVVWEYNVQPGDITAPARALSGGNLQKLVIGREFFR 434

Query: 426 NPNVLVLIDPTAGVDVKSKEALLSVVDRVREEGKAVLVVSGELDD-LRTCDRVLVMFRGR 484
            P V+V  +PT G+D+ + E +   +   R     VL+V+G+L++ L   DR+ VM+RGR
Sbjct: 435 KPEVIVAENPTQGLDISATEEVWGRLLEARST-SGVLLVTGDLNEALELADRIAVMYRGR 493

Query: 485 VAAEFPAGWQDHDLIASVEGVSL 507
               F     D D  A V+ + L
Sbjct: 494 FIDVF-----DKDDTAKVQAIGL 511


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: 692
Number of extensions: 38
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: 537
Length adjustment: 35
Effective length of query: 475
Effective length of database: 502
Effective search space:   238450
Effective search space used:   238450
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