GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lacK in Acidovorax sp. GW101-3H11

Align LacK, component of Lactose porter (characterized)
to candidate Ac3H11_2066 SN-glycerol-3-phosphate transport ATP-binding protein UgpC (TC 3.A.1.1.3)

Query= TCDB::Q01937
         (363 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_2066
          Length = 355

 Score =  296 bits (757), Expect = 7e-85
 Identities = 165/356 (46%), Positives = 224/356 (62%), Gaps = 19/356 (5%)

Query: 6   LTDIRKSYG----SLEVIKGVNLEVSSGEFVVFVGPSGCGKSTLLRMIAGLEDISSGELT 61
           +  I K +G    S+EV++ V++ V+ GEF++ VGPSGCGKSTLL +IAGL++ + GE+ 
Sbjct: 7   IAGINKRFGKGDKSVEVLRKVDIHVAPGEFLILVGPSGCGKSTLLNIIAGLDEPTEGEIR 66

Query: 62  IGGTVMNDVDPSKRGIAMVFQTYALYPHMTVRENMGFALRFAGMAKDEIERRVNAAAKIL 121
           IGG  +  + P  R IAMVFQ+YALYP ++V +N+GFAL    M K E ++R++  A +L
Sbjct: 67  IGGKNVVGMPPRDRDIAMVFQSYALYPTLSVADNIGFALEMRKMPKPERQKRIDEVAAML 126

Query: 122 ELDALMDRKPKALSGGQRQRVAIGRAIVRQPDVFLFDEPLSNLDAELRVHMRVEIARLHK 181
           ++  L+DR+P  LSGGQRQRVA+GRA+ RQP +FLFDEPLSNLDA+LRV MR EI RLH+
Sbjct: 127 QISHLLDRRPSQLSGGQRQRVAMGRALARQPQLFLFDEPLSNLDAKLRVEMRAEIKRLHQ 186

Query: 182 ELNATIVYVTHDQVEAMTLADKIVVMRGGIVEQVGAPLALYDDPDNMFVAGFIGSPRMNF 241
               T VYVTHDQVEAMTL  +I VM+GG+V+Q+G P  +Y+ P N +VA FIGSP MN 
Sbjct: 187 ASGITSVYVTHDQVEAMTLGSRIAVMKGGVVQQLGTPDEIYNRPANTYVATFIGSPTMNL 246

Query: 242 LPAVVIGQAEGGQVTVALKARPDTQLTVACATPPQGGDAVTVGVRPEHFLPAGSGDTQLT 301
           L   V G   G Q   AL   P          PP   + V +GVRPEH +   +   +  
Sbjct: 247 LRGAVTGGQFGIQ-GAALNLAP----------PPSSANEVLLGVRPEHLVMQETAPWR-- 293

Query: 302 AHVDVVEHLGNTSYVYAHTVPGEQIIIEQEERRHGGRYGDEIAVGISAKTSFLFDA 357
             V VVE  G  +YV   T  G   +    + R   + G+ + + ++   +  FDA
Sbjct: 294 GRVSVVEPTGPDTYVMVDTAAGSVTLRTDAQTR--VQPGEHVGLALAPAHAHWFDA 347


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: 366
Number of extensions: 9
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: 355
Length adjustment: 29
Effective length of query: 334
Effective length of database: 326
Effective search space:   108884
Effective search space used:   108884
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