GapMind for catabolism of small carbon sources

 

Alignments for a candidate for thuK in Phaeacidiphilus oryzae TH49

Align Trehalose import ATP-binding protein SugC; EC 7.5.2.- (characterized)
to candidate WP_037573817.1 BS73_RS18100 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC

Query= SwissProt::P9WQI3
         (393 letters)



>NCBI__GCF_000744815.1:WP_037573817.1
          Length = 369

 Score =  352 bits (902), Expect = e-101
 Identities = 190/322 (59%), Positives = 226/322 (70%), Gaps = 4/322 (1%)

Query: 1   MAEIVLDHVNKSYPDGHT-AVRDLNLTIADGEFLILVGPSGCGKTTTLNMIAGLEDISSG 59
           MA +  D   + YP G   AV  L+L IADGEFL+LVGPSGCGK+T+L M+AGLED+++G
Sbjct: 1   MATVTYDKATRIYPGGDKPAVDALDLEIADGEFLVLVGPSGCGKSTSLRMLAGLEDVNNG 60

Query: 60  ELRIAGERVNEKAPKDRDIAMVFQSYALYPHMTVRQNIAFPLTLAKMRKADIAQKVSETA 119
            +RI    V    PKDRDIAMVFQ+YALYPHMTV  N+ F L +A + KA+I  KV E A
Sbjct: 61  AIRIGERDVTHLPPKDRDIAMVFQNYALYPHMTVADNMGFALKIAGVNKAEIRSKVEEAA 120

Query: 120 KILDLTNLLDRKPSQLSGGQRQRVAMGRAIVRHPKAFLMDEPLSNLDAKLRVQMRGEIAQ 179
           KILDLT  LDRKP  LSGGQRQRVAMGRAIVR P+ FLMDEPLSNLDAKLRV  R +IA 
Sbjct: 121 KILDLTEFLDRKPKALSGGQRQRVAMGRAIVREPQVFLMDEPLSNLDAKLRVSTRTQIAG 180

Query: 180 LQRRLGTTTVYVTHDQTEAMTLGDRVVVMYGGIAQQIGTPEELYERPANLFVAGFIGSPA 239
           LQRRLG TTVYVTHDQ EAMT+GDRV V+  G+ QQ+ TP  +Y+RPANLFVAGFIGSPA
Sbjct: 181 LQRRLGITTVYVTHDQVEAMTMGDRVAVLKDGLLQQVDTPRNMYDRPANLFVAGFIGSPA 240

Query: 240 MNFFPARLTAIGLTLPFGEVTLAPEVQGVIAAHPKPENVIVGVRPEHIQDAALIDAYQRI 299
           MN     +T  G+      V ++ +  G  AA+   + V VGVRPEH+      +     
Sbjct: 241 MNLVEVPITDGGVKFGESVVQVSRDAVGE-AANAGDKTVTVGVRPEHLDIVGGTEGGGED 299

Query: 300 RALTFQVKVNLVESLGADKYLY 321
           + L   V VN+VE LGAD Y+Y
Sbjct: 300 KGLA--VTVNVVEELGADGYVY 319


Lambda     K      H
   0.319    0.135    0.377 

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: 428
Number of extensions: 19
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: 393
Length of database: 369
Length adjustment: 30
Effective length of query: 363
Effective length of database: 339
Effective search space:   123057
Effective search space used:   123057
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: 50 (23.9 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