GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lacK in Desulfovibrio vulgaris Miyazaki F

Align ABC transporter for Lactose, ATPase component (characterized)
to candidate 8500851 DvMF_1589 ABC transporter related (RefSeq)

Query= reanno::Smeli:SM_b20002
         (358 letters)



>FitnessBrowser__Miya:8500851
          Length = 354

 Score =  229 bits (585), Expect = 6e-65
 Identities = 133/345 (38%), Positives = 196/345 (56%), Gaps = 17/345 (4%)

Query: 1   MSELQLSDVRKSYGGLEVIKGVDLDIKSGEFVVFVGPSGCGKSTLLRMIAGLEEISSGDL 60
           MS ++L +V K +GG+  +  ++L+I  GE    +GPSGCGK+T LRM+AG E++  G++
Sbjct: 1   MSYVRLVNVTKRFGGVTAVDSLNLEIGRGECFSMLGPSGCGKTTTLRMVAGFEDLDDGEI 60

Query: 61  TIDD----VRMND--VDPSKRGIAMVFQSYALYPHMTVRENMGFALRFAGVPRAEIEKRV 114
            + D     R N+  + P KR   MVFQ++A++PH++V EN+ F LR   +  AEI++R 
Sbjct: 61  HVGDRLLSARRNNYYLPPEKRDFGMVFQAFAVWPHLSVYENVAFPLRIRRLSAAEIDRRT 120

Query: 115 NEAAHILELGALLDRKPKQLSGGQRQRVAIGRAIVRHPKIFLFDEPLSNLDAELRVHMRI 174
            EA H   L  +  + P  LSGG +QRVA+ RA+  +P + L DEPLS+LD  LR  MR 
Sbjct: 121 REALHHTSLADVAQKSPDDLSGGGKQRVALARALAINPDVMLLDEPLSSLDPHLREEMRF 180

Query: 175 EIARLHKQLATTIVYVTHDQVEAMTLADKIVVMRAGVVEQVGSPLDLYDDPANLFVAGFI 234
           EI  L +    +I+YVTHDQ EAM L+D+I+VMR GVV+QVG+PLD+Y +PAN FV GFI
Sbjct: 181 EIKDLQRTFGFSILYVTHDQSEAMALSDRIMVMRNGVVQQVGTPLDVYTNPANSFVFGFI 240

Query: 235 GSPKMNFLKGVIEIDEDQAYARLPDYGDAKI----PVTLQAAAGTAVTIGIRPEHFDEAG 290
           G      L   ++++         + GDA++    P + +  +     +  RP   D   
Sbjct: 241 G------LSNFLDVNLTPEGLVRVNGGDARVTPATPPSARLVSAGRAALASRPSEIDFTA 294

Query: 291 PAALDLAIDMLEHLGGETFAYARHHGNGELIVVETKNGRGLKTGD 335
              L   +    +L GE   Y       E+ V + +   G   GD
Sbjct: 295 EGGLRGVVRRRAYL-GEIVDYRIDVSGQEVRVQKGRRAPGPAEGD 338


Lambda     K      H
   0.321    0.139    0.396 

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: 342
Number of extensions: 13
Number of successful extensions: 2
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: 358
Length of database: 354
Length adjustment: 29
Effective length of query: 329
Effective length of database: 325
Effective search space:   106925
Effective search space used:   106925
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: 49 (23.5 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