GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HSERO_RS17020 in Phaeacidiphilus oryzae TH49

Align ABC-type sugar transport system, ATPase component protein (characterized, see rationale)
to candidate WP_037573817.1 BS73_RS18100 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC

Query= uniprot:D8IPI1
         (406 letters)



>NCBI__GCF_000744815.1:WP_037573817.1
          Length = 369

 Score =  295 bits (755), Expect = 1e-84
 Identities = 172/372 (46%), Positives = 228/372 (61%), Gaps = 12/372 (3%)

Query: 1   MADIHCQALAKHYAGGP-PVLHPLDLHIGDGEFVVLLGPSGCGKSTMLRMIAGLEDISGG 59
           MA +      + Y GG  P +  LDL I DGEF+VL+GPSGCGKST LRM+AGLED++ G
Sbjct: 1   MATVTYDKATRIYPGGDKPAVDALDLEIADGEFLVLVGPSGCGKSTSLRMLAGLEDVNNG 60

Query: 60  TLRIGGTVVNDLPARERNVAMVFQNYALYPHMSVYDNIAFGLRRLKRPAAEIDRRVREVA 119
            +RIG   V  LP ++R++AMVFQNYALYPHM+V DN+ F L+      AEI  +V E A
Sbjct: 61  AIRIGERDVTHLPPKDRDIAMVFQNYALYPHMTVADNMGFALKIAGVNKAEIRSKVEEAA 120

Query: 120 ALLNLEALLERKPRAMSGGQQQRAAIARAIIKTPSVFLFDEPLSNLDAKLRAQLRGDIKR 179
            +L+L   L+RKP+A+SGGQ+QR A+ RAI++ P VFL DEPLSNLDAKLR   R  I  
Sbjct: 121 KILDLTEFLDRKPKALSGGQRQRVAMGRAIVREPQVFLMDEPLSNLDAKLRVSTRTQIAG 180

Query: 180 LHQRLRTTTVYVTHDQLEAMTLADRVILMQDGRIVQAGSPAELYRYPRNLFAAGFIGTPA 239
           L +RL  TTVYVTHDQ+EAMT+ DRV +++DG + Q  +P  +Y  P NLF AGFIG+PA
Sbjct: 181 LQRRLGITTVYVTHDQVEAMTMGDRVAVLKDGLLQQVDTPRNMYDRPANLFVAGFIGSPA 240

Query: 240 MNFLSGTVQRQDGQLFIETAHQRWALTGERFSRLRHA--MAVKLAVRPDHVRIAGEREPA 297
           MN +   +    G  F E+  Q   ++ +      +A    V + VRP+H+ I G  E  
Sbjct: 241 MNLVEVPI-TDGGVKFGESVVQ---VSRDAVGEAANAGDKTVTVGVRPEHLDIVGGTEGG 296

Query: 298 A-SLTCPVSVELVEILGADALL--TTRCGDQT--LTALVPADRLPQPGATLTLALDQHEL 352
                  V+V +VE LGAD  +  + + G +T  L   V    +P  G  L +     E 
Sbjct: 297 GEDKGLAVTVNVVEELGADGYVYGSAKVGTETIDLVVRVGGRDIPMKGDQLRVVPRAGET 356

Query: 353 HVFDVESGENLS 364
           HVF   +G+ LS
Sbjct: 357 HVFSTSTGKRLS 368


Lambda     K      H
   0.321    0.137    0.403 

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: 400
Number of extensions: 13
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: 406
Length of database: 369
Length adjustment: 30
Effective length of query: 376
Effective length of database: 339
Effective search space:   127464
Effective search space used:   127464
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