GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SMc02869 in Phaeacidiphilus oryzae TH49

Align N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized)
to candidate WP_037573817.1 BS73_RS18100 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC

Query= reanno::Smeli:SMc02869
         (352 letters)



>NCBI__GCF_000744815.1:WP_037573817.1
          Length = 369

 Score =  309 bits (792), Expect = 7e-89
 Identities = 174/346 (50%), Positives = 222/346 (64%), Gaps = 36/346 (10%)

Query: 30  GSHEVLKGIDLDVKDGEFVIFVGPSGCGKSTLLRTIAGLEDATSGSVQIDGVEVGHVAPA 89
           G    +  +DL++ DGEF++ VGPSGCGKST LR +AGLED  +G+++I   +V H+ P 
Sbjct: 16  GDKPAVDALDLEIADGEFLVLVGPSGCGKSTSLRMLAGLEDVNNGAIRIGERDVTHLPPK 75

Query: 90  KRGIAMVFQSYALYPHLTVKDNMGLGLKQAGVPKAEIEEKVAKAAGMLSLEPYLARRPAE 149
            R IAMVFQ+YALYPH+TV DNMG  LK AGV KAEI  KV +AA +L L  +L R+P  
Sbjct: 76  DRDIAMVFQNYALYPHMTVADNMGFALKIAGVNKAEIRSKVEEAAKILDLTEFLDRKPKA 135

Query: 150 LSGGQRQRVAIGRAIVREPKLFLFDEPLSNLDAALRVNTRLEIARLHRSLKATMIYVTHD 209
           LSGGQRQRVA+GRAIVREP++FL DEPLSNLDA LRV+TR +IA L R L  T +YVTHD
Sbjct: 136 LSGGQRQRVAMGRAIVREPQVFLMDEPLSNLDAKLRVSTRTQIAGLQRRLGITTVYVTHD 195

Query: 210 QVEAMTLADKIVVLNAGRIEQVGSPMELYNRPANLFVAGFIGSPQMNFI----------- 258
           QVEAMT+ D++ VL  G ++QV +P  +Y+RPANLFVAGFIGSP MN +           
Sbjct: 196 QVEAMTMGDRVAVLKDGLLQQVDTPRNMYDRPANLFVAGFIGSPAMNLVEVPITDGGVKF 255

Query: 259 -------------EAAKLGDGEAKTIGIRPEH---IGLSRESGDWKGKVIH---VEHLGA 299
                        EAA  GD +  T+G+RPEH   +G +   G+ KG  +    VE LGA
Sbjct: 256 GESVVQVSRDAVGEAANAGD-KTVTVGVRPEHLDIVGGTEGGGEDKGLAVTVNVVEELGA 314

Query: 300 DTIIY----IESETVGLLTVRLFGEHRYATDDIVHATPVIGSMHRF 341
           D  +Y    + +ET+ L+ VR+ G       D +   P  G  H F
Sbjct: 315 DGYVYGSAKVGTETIDLV-VRVGGRDIPMKGDQLRVVPRAGETHVF 359


Lambda     K      H
   0.320    0.137    0.393 

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: 365
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: 352
Length of database: 369
Length adjustment: 29
Effective length of query: 323
Effective length of database: 340
Effective search space:   109820
Effective search space used:   109820
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