GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malK_Aa in Geotalea uraniireducens Rf4

Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate WP_011938227.1 GURA_RS06655 ABC transporter ATP-binding protein

Query= BRENDA::Q70HW1
         (384 letters)



>NCBI__GCF_000016745.1:WP_011938227.1
          Length = 353

 Score =  225 bits (573), Expect = 2e-63
 Identities = 125/252 (49%), Positives = 167/252 (66%), Gaps = 9/252 (3%)

Query: 21  VKDFNLDIQDKEFTVFVGPSGCGKTTTLRMIAGLEDITEGNLYIGDRRVND------VPP 74
           +K  +LD+   E    +GPSG GKTT LR IAGLE  + G++ IG++ V +      V  
Sbjct: 21  LKGVSLDVNKGEIVALLGPSGSGKTTLLRSIAGLELPSHGSIRIGEQMVFESAKKIEVSV 80

Query: 75  KDRDIAMVFQNYALYPHMTVYQNMAFGLKLRKVPKAEIDRRVQEAAKILDIAHLLDRKPK 134
           + R +  VFQ+YAL+PH TVY+N+A+GLKLRKVP  EI +RVQE    L +  L +R P 
Sbjct: 81  EKRCLGFVFQSYALWPHRTVYENVAYGLKLRKVPDGEIRQRVQEVLANLGLGDLSERHPH 140

Query: 135 ALSGGQRQRVALGRAIVREPQVFLMDEPLSNLDAKLRVQMRAEIRKLHQRLQTTVIYVTH 194
            LSGGQ+QRVAL R++V  PQV L+DEPLSNLDAKLR + R  +R+L   L  + + VTH
Sbjct: 141 QLSGGQQQRVALARSLVYNPQVILLDEPLSNLDAKLREEARIWLRQLIIDLNLSAVCVTH 200

Query: 195 DQTEAMTMGDRIVVMRDGVIQQADTPQVVYSQPKNMFVAGFIGSPAMNFIRGEIVQ-DGD 253
           DQ EAM M D++V+++DGVI+QA TPQ +Y  PK++FVA F+G  A N I G +   DGD
Sbjct: 201 DQAEAMAMADKVVLLKDGVIEQAGTPQEMYGAPKSLFVAEFMG--ANNTISGLVTDVDGD 258

Query: 254 AFYFRAPSISLR 265
           +        +LR
Sbjct: 259 SARIEGNGWALR 270


Lambda     K      H
   0.321    0.138    0.395 

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: 369
Number of extensions: 10
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: 384
Length of database: 353
Length adjustment: 30
Effective length of query: 354
Effective length of database: 323
Effective search space:   114342
Effective search space used:   114342
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 Apr 09 2024. 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