GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lacK in Azospirillum brasilense Sp245

Align LacK, component of Lactose porter (characterized)
to candidate AZOBR_RS25595 AZOBR_RS25595 sugar ABC transporter ATP-binding protein

Query= TCDB::Q01937
         (363 letters)



>FitnessBrowser__azobra:AZOBR_RS25595
          Length = 358

 Score =  361 bits (926), Expect = e-104
 Identities = 198/362 (54%), Positives = 250/362 (69%), Gaps = 4/362 (1%)

Query: 1   MAEVRLTDIRKSYGSLEVIKGVNLEVSSGEFVVFVGPSGCGKSTLLRMIAGLEDISSGEL 60
           MA V L  +RKS+G +EVI GV+LEV+ GEFV FVGPSGCGKSTLLR+IAGLE+ S G+L
Sbjct: 1   MAGVTLRGVRKSFGRIEVIHGVDLEVADGEFVAFVGPSGCGKSTLLRLIAGLEEPSGGDL 60

Query: 61  TIGGTVMNDVDPSKRGIAMVFQTYALYPHMTVRENMGFALRFAGMAKDEIERRVNAAAKI 120
           +IGG  +ND  P+ RGIAMVFQ+YALYPHMT  +NM F L  +   K  I  RV AAA++
Sbjct: 61  SIGGQRVNDRPPAARGIAMVFQSYALYPHMTAYDNMAFGLTLSRTDKGTIAERVRAAARL 120

Query: 121 LELDALMDRKPKALSGGQRQRVAIGRAIVRQPDVFLFDEPLSNLDAELRVHMRVEIARLH 180
           L+++ L+DRKP+ LSGGQRQRVAIGRAIVR+P VFLFDEPLSNLDA LRV MR+EIA+L 
Sbjct: 121 LQIEDLLDRKPRDLSGGQRQRVAIGRAIVREPQVFLFDEPLSNLDAGLRVQMRLEIAKLK 180

Query: 181 KELNATIVYVTHDQVEAMTLADKIVVMRGGIVEQVGAPLALYDDPDNMFVAGFIGSPRMN 240
            +L AT++YVTHDQVEAMTLAD+IVV+  G VEQ G PL LY  P N FVAGFIGSP MN
Sbjct: 181 ADLRATMIYVTHDQVEAMTLADRIVVLNAGRVEQAGTPLELYHRPRNRFVAGFIGSPAMN 240

Query: 241 FLPAVVIGQAEGGQVTVALKARPDTQLTVACATPPQGGDAVTVGVRPEHFLPAGSGDTQL 300
           FL  V  G  + G V V L       + V  A  P  G  +T+GVRPEH +    G   L
Sbjct: 241 FLDVVSEGLTD-GSVRVWLPGGVPLDIAVDGAA-PAAGTPLTLGVRPEH-VGLADGGAGL 297

Query: 301 TAHVDVVEHLGNTSYVYAHTVPGEQIIIEQEERRHGGRYGDEIAVGISAKTSFLFDASGR 360
            A +  VE LG  ++ +A    G+++++  +  R     G+ + + +  +T+ LF   G+
Sbjct: 298 LATILAVERLGGETHCHAALEDGQRLLVRLDGDRPVAA-GERLRLNLRGETAHLFGPDGQ 356

Query: 361 RI 362
           R+
Sbjct: 357 RL 358


Lambda     K      H
   0.320    0.137    0.390 

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: 432
Number of extensions: 18
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: 363
Length of database: 358
Length adjustment: 29
Effective length of query: 334
Effective length of database: 329
Effective search space:   109886
Effective search space used:   109886
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