GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livJ in Desulfovibrio vulgaris Miyazaki F

Align Leucine-, isoleucine-, valine-, threonine-, and alanine-binding protein; LIVAT-BP; Leu/Ile/Val/Thr/Ala-binding protein (characterized)
to candidate 8502037 DvMF_2750 Extracellular ligand-binding receptor (RefSeq)

Query= SwissProt::P21175
         (373 letters)



>FitnessBrowser__Miya:8502037
          Length = 375

 Score =  205 bits (522), Expect = 1e-57
 Identities = 126/367 (34%), Positives = 201/367 (54%), Gaps = 15/367 (4%)

Query: 8   LSRLFAAMAIAGFASYSMAADT----IKIALAGPVTGPVAQYGDMQRAGALMAIEQINKA 63
           +  +  A+ +A  AS  MAA      +KI L  P+TG  A  G   R    +  +++NKA
Sbjct: 1   MKHVVKALTLALAASLLMAATAFAAPVKIGLMCPLTGKWASEGQDMRNIVTLLADELNKA 60

Query: 64  GGVNGAQLEGVIYDDACDPKQAVAVANKVVNDGVKFVVGHVCSSSTQPATDIYEDEGVLM 123
           GG+NG ++E V+ DD  DP+ A   A K+   GV   +G   S+ T+ +  IY++ GV+ 
Sbjct: 61  GGINGNKVELVVEDDGGDPRTAALAAQKLTTSGVIAAIGTYGSAVTEASQSIYDEAGVVQ 120

Query: 124 ITPSATAPEITSRGYKLIFRTIGLDNMQGPVAGKFI-AERYKDKTIAVLHDKQQYGEGIA 182
           I   +TA  +T +G K   RT   D+ QG VA K I A+ Y  K +A+LHD   Y +G+A
Sbjct: 121 IATGSTAVRLTEKGLKRFLRTAPRDDEQGMVAAKLIKAKGY--KAVALLHDNSSYAKGLA 178

Query: 183 TEVKKTVEDAGIKVAVFEGLNAGDKDFNALISKLKKAGVQFVYFGGYHPEMGLLLRQAKQ 242
            E K  ++ AG K+  ++ L  G++D+ A+++KLK A    ++  GY+PE+G+LLRQ  +
Sbjct: 179 DETKALLDKAGTKIVFYDALTPGERDYTAILTKLKAANPDIIFCTGYYPEVGMLLRQKME 238

Query: 243 AGLDARFMGPEGVGNSEITAIAG-DASEGMLATLPRAFEQD---PKNKALIDAFKAK-NQ 297
              +   MG +   ++++  I+G +A++G     P    QD   P  K+++ A+KAK N 
Sbjct: 239 MKWNVPMMGGDAANHADLVKISGKEAAKGYFFLSPPG-PQDLDAPAAKSMLTAYKAKYNG 297

Query: 298 DPSGIFVLPAYSAVTVIAKGIEKAGEADPEKVAEALRANTFETP--TGNLGFDEKGDLKN 355
            P  ++ + A  A  VI + ++  G+AD   +AE L+      P  TG + F+EKGD   
Sbjct: 298 VPGSVWSVLAGDAFNVIVEAVKSTGKADSGAIAEYLKTKLKNYPGFTGQISFNEKGDRVG 357

Query: 356 FDFTVYE 362
             + VYE
Sbjct: 358 DLYRVYE 364


Lambda     K      H
   0.316    0.133    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: 338
Number of extensions: 19
Number of successful extensions: 4
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: 373
Length of database: 375
Length adjustment: 30
Effective length of query: 343
Effective length of database: 345
Effective search space:   118335
Effective search space used:   118335
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 (21.6 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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