GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lacK in Halococcus hamelinensis 100A6

Align LacK, component of Lactose porter (characterized)
to candidate WP_007692556.1 C447_RS07635 ABC transporter ATP-binding protein

Query= TCDB::Q01937
         (363 letters)



>NCBI__GCF_000336675.1:WP_007692556.1
          Length = 362

 Score =  286 bits (731), Expect = 8e-82
 Identities = 163/359 (45%), Positives = 222/359 (61%), Gaps = 19/359 (5%)

Query: 4   VRLTDIRKSYGSLEVIKGVNLEVSSGEFVVFVGPSGCGKSTLLRMIAGLEDISSGELTIG 63
           V L++I K +GS+  +  V+L + +GEF++ VGPSGCGK+T LRMIAGLE  SSG +   
Sbjct: 3   VELSNISKRFGSIVAVDDVSLTIENGEFLILVGPSGCGKTTTLRMIAGLEKPSSGRIYFD 62

Query: 64  GTVMNDVDPSKRGIAMVFQTYALYPHMTVRENMGFALRFAGMAKDEIERRVNAAAKILEL 123
           G  +    P +R IA VFQ YALYPHMT R+NM FAL    +  DE+ +RV + A  L +
Sbjct: 63  GDDVTQFSPQQRHIAFVFQNYALYPHMTTRKNMSFALEDQDIPSDEVAQRVTSTADKLGI 122

Query: 124 DALMDRKPKALSGGQRQRVAIGRAIVRQPDVFLFDEPLSNLDAELRVHMRVEIARLHKEL 183
              +D++P  LSGGQ+QRVA+GR+IVR P VFL DEPLSNLDA+LR +MR E+  LH++L
Sbjct: 123 TDQLDQRPGELSGGQQQRVALGRSIVRNPSVFLLDEPLSNLDAKLRTNMRAELQELHQDL 182

Query: 184 NATIVYVTHDQVEAMTLADKIVVMRGGIVEQVGAPLALYDDPDNMFVAGFIGSPRMNFLP 243
             T+VYVTHDQ EAMT+ D+I VM  G ++QV  P   Y+ P N FVAGFIGSP MNF  
Sbjct: 183 ETTMVYVTHDQEEAMTMGDRIAVMDEGTIQQVAPPNEAYNQPANRFVAGFIGSPSMNFFD 242

Query: 244 AVVIGQAEGGQVTVALKARPDTQLTVACATPPQ-GGDAVTVGVRPE--HFLPAGSGDTQL 300
           A      + G+V    +A P T       TP +  G    +G+RPE     P  +G+  +
Sbjct: 243 A----SLDDGRV----RAGPFT-----LPTPDRVSGPLSELGIRPEDVSVTPTATGE-DV 288

Query: 301 TAHVDVVEHLGNTSYVYAHTVPGEQIIIEQEERRHGGRYGDEIAVGISAKTSFLFDASG 359
           +A V V E +G+++ +Y   + GE +I E +        GD++ V +  +   LFD  G
Sbjct: 289 SATVTVFEQVGSSNIIYLE-IDGETMIAETDASVQLAP-GDDVGVSLDTERVHLFDRGG 345


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: 364
Number of extensions: 12
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: 362
Length adjustment: 29
Effective length of query: 334
Effective length of database: 333
Effective search space:   111222
Effective search space used:   111222
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 24 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