GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aglK' in Phaeacidiphilus oryzae TH49

Align Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale)
to candidate WP_037573817.1 BS73_RS18100 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC

Query= uniprot:A8LLL2
         (373 letters)



>NCBI__GCF_000744815.1:WP_037573817.1
          Length = 369

 Score =  281 bits (719), Expect = 2e-80
 Identities = 172/356 (48%), Positives = 221/356 (62%), Gaps = 27/356 (7%)

Query: 14  GDVKVLSNINLDIQQGELIVFVGPSGCGKSTLLRMIAGLEKITGGTLEIDGTVVNDVPPA 73
           GD   +  ++L+I  GE +V VGPSGCGKST LRM+AGLE +  G + I    V  +PP 
Sbjct: 16  GDKPAVDALDLEIADGEFLVLVGPSGCGKSTSLRMLAGLEDVNNGAIRIGERDVTHLPPK 75

Query: 74  QRGIAMVFQSYALYPHMTVRENMSFALKIAKKSQAEIDAAVEAAAEKLQLGQYLDRLPKA 133
            R IAMVFQ+YALYPHMTV +NM FALKIA  ++AEI + VE AA+ L L ++LDR PKA
Sbjct: 76  DRDIAMVFQNYALYPHMTVADNMGFALKIAGVNKAEIRSKVEEAAKILDLTEFLDRKPKA 135

Query: 134 LSGGQRQRVAIGRSIVRDPKVYLFDEPLSNLDAALRVATRLEIAQLKEAMPESTMVYVTH 193
           LSGGQRQRVA+GR+IVR+P+V+L DEPLSNLDA LRV+TR +IA L+  +  +T VYVTH
Sbjct: 136 LSGGQRQRVAMGRAIVREPQVFLMDEPLSNLDAKLRVSTRTQIAGLQRRLGITT-VYVTH 194

Query: 194 DQVEAMTLATRIVVLAGGGIAQVGSPLELYEKPENEFVAQFIGSPKMNLLPGKIIGTGAQ 253
           DQVEAMT+  R+ VL  G + QV +P  +Y++P N FVA FIGSP MNL+          
Sbjct: 195 DQVEAMTMGDRVAVLKDGLLQQVDTPRNMYDRPANLFVAGFIGSPAMNLV---------- 244

Query: 254 TTVEMTDGGRAVSD---YPSDDSLMGAA------VNVGVRPE--DMVEAAPGG--DYVFE 300
             V +TDGG    +     S D++  AA      V VGVRPE  D+V    GG  D    
Sbjct: 245 -EVPITDGGVKFGESVVQVSRDAVGEAANAGDKTVTVGVRPEHLDIVGGTEGGGEDKGLA 303

Query: 301 GKVAITEALGEVTLLYFEAPSGED--PTIGKLQGIHKDLKGQVTRLTAEPAKVHVF 354
             V + E LG    +Y  A  G +    + ++ G    +KG   R+     + HVF
Sbjct: 304 VTVNVVEELGADGYVYGSAKVGTETIDLVVRVGGRDIPMKGDQLRVVPRAGETHVF 359


Lambda     K      H
   0.316    0.135    0.379 

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: 430
Number of extensions: 20
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: 373
Length of database: 369
Length adjustment: 30
Effective length of query: 343
Effective length of database: 339
Effective search space:   116277
Effective search space used:   116277
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 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