GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aglK in Phaeacidiphilus oryzae TH49

Align ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized)
to candidate WP_037573817.1 BS73_RS18100 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC

Query= reanno::Smeli:SMc03065
         (362 letters)



>NCBI__GCF_000744815.1:WP_037573817.1
          Length = 369

 Score =  306 bits (785), Expect = 4e-88
 Identities = 178/351 (50%), Positives = 228/351 (64%), Gaps = 12/351 (3%)

Query: 14  GAVDVIHGIDLDIKEGEFVVFVGPSGCGKSTLLRMIAGLEEITGGDMFIDGERVNDVPPS 73
           G    +  +DL+I +GEF+V VGPSGCGKST LRM+AGLE++  G + I    V  +PP 
Sbjct: 16  GDKPAVDALDLEIADGEFLVLVGPSGCGKSTSLRMLAGLEDVNNGAIRIGERDVTHLPPK 75

Query: 74  KRGIAMVFQSYALYPHMTVYDNMAFGMRIARESKEEIDRRVRGAADMLQLTPYLDRLPKA 133
            R IAMVFQ+YALYPHMTV DNM F ++IA  +K EI  +V  AA +L LT +LDR PKA
Sbjct: 76  DRDIAMVFQNYALYPHMTVADNMGFALKIAGVNKAEIRSKVEEAAKILDLTEFLDRKPKA 135

Query: 134 LSGGQRQRVAIGRAICRNPKVFLFDEPLSNLDAALRVATRIEIAKLSERMSDTTMIYVTH 193
           LSGGQRQRVA+GRAI R P+VFL DEPLSNLDA LRV+TR +IA L  R+  TT +YVTH
Sbjct: 136 LSGGQRQRVAMGRAIVREPQVFLMDEPLSNLDAKLRVSTRTQIAGLQRRLGITT-VYVTH 194

Query: 194 DQVEAMTLADRIVVLSAGHIEQVGAPLELYERPANLFVARFIGSPAMNVIPATITATGQQ 253
           DQVEAMT+ DR+ VL  G ++QV  P  +Y+RPANLFVA FIGSPAMN++   IT  G +
Sbjct: 195 DQVEAMTMGDRVAVLKDGLLQQVDTPRNMYDRPANLFVAGFIGSPAMNLVEVPITDGGVK 254

Query: 254 TAVSLAGGKSVTLDVPTNASENG-KTASFGVRPEDLRV---TE--ADDFLFEGTVSIVEA 307
              S+     V+ D    A+  G KT + GVRPE L +   TE   +D     TV++VE 
Sbjct: 255 FGESVV---QVSRDAVGEAANAGDKTVTVGVRPEHLDIVGGTEGGGEDKGLAVTVNVVEE 311

Query: 308 LGEVTLLYIEGLVENEPI--IAKMPGIARVGRGDKVRFTADKAKLHLFDTN 356
           LG    +Y    V  E I  + ++ G     +GD++R      + H+F T+
Sbjct: 312 LGADGYVYGSAKVGTETIDLVVRVGGRDIPMKGDQLRVVPRAGETHVFSTS 362


Lambda     K      H
   0.320    0.137    0.387 

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: 414
Number of extensions: 16
Number of successful extensions: 3
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: 362
Length of database: 369
Length adjustment: 30
Effective length of query: 332
Effective length of database: 339
Effective search space:   112548
Effective search space used:   112548
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