GapMind for catabolism of small carbon sources

 

Alignments for a candidate for frcA in Phyllobacterium brassicacearum STM 196

Align ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale)
to candidate WP_106714515.1 CU102_RS28785 sugar ABC transporter ATP-binding protein

Query= uniprot:A0A0C4Y5F6
         (540 letters)



>NCBI__GCF_003010955.1:WP_106714515.1
          Length = 513

 Score =  383 bits (984), Expect = e-111
 Identities = 217/503 (43%), Positives = 314/503 (62%), Gaps = 14/503 (2%)

Query: 13  LLALRNICKTFPGVRALRKVELTAYAGEVHALMGENGAGKSTLMKILSGAYTADPGGECH 72
           LL   NI K FPGV AL  V+     G VHALMGENGAGKSTLMKIL+G Y  D G E +
Sbjct: 23  LLNAENIRKEFPGVLALDNVQFRLKRGTVHALMGENGAGKSTLMKILAGIYIPDQG-EVY 81

Query: 73  IDGQRVQIDGPQSARDLGVAVIYQELSLAPNLSVAENIYLGRALQRR-GLVARGDMVRAC 131
           + G  +++  P  A + G+A+I+QEL+L P ++VAENI++ R  +   G V  G M    
Sbjct: 82  LKGLPIRLKSPLDALENGIAMIHQELNLMPFMTVAENIWIRREPKNGFGFVDHGKMYDMT 141

Query: 132 APTLARLGADFSPAANVASLSIAQRQLVEIARAVHFEARILVMDEPTTPLSTHETDRLFA 191
           A    RL     P + V  LS+A RQ+VEIA+AV +E+ +L+MDEPT+ L+  E + LF 
Sbjct: 142 ADLFKRLNITLDPESQVRDLSVANRQMVEIAKAVSYESDVLIMDEPTSALTEREVEHLFQ 201

Query: 192 LIRQLRGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHLSQAALVKMMVGRDL 251
           +IR LR +G+ I+YI+H+M E+ E+AD  +V RDG ++GT     +++  ++KMMVGR++
Sbjct: 202 IIRDLREQGIGIVYITHKMNELFEIADEFSVFRDGRYIGTHASTDVTRDDIIKMMVGREI 261

Query: 252 SGFYTKTHGQAVEREVMLSVRDVADGRRVKGCSFDLRAGEVLGLAGLVGAGRTELARLVF 311
           +  + K        +V+LSV+D++        SFD+RAGE+LG+AGLVG+GR+ +A  +F
Sbjct: 262 TQMFPKEIVPI--GDVVLSVKDLSLKNVFHDVSFDVRAGEILGVAGLVGSGRSNVAETIF 319

Query: 312 GADARTRGEVRIANPAGSGGLVTLPAGGPRQAIDAGIAYLTEDRKLQGLFLDQSVHENIN 371
           G    T G + I           +    P QAI  G+A++TEDRK  G  L   V EN+ 
Sbjct: 320 GVTPATSGTITIKGQP-------IKMNSPTQAISHGMAFITEDRKETGCLLILDVLENMQ 372

Query: 372 LIVAARDALGLGRLNRTAARRRTTEAIDTLGIRVAHAQVNVGALSGGNQQKVMLSRLLEI 431
           + V     +  G +      +      DTL ++    +  V  LSGGNQQKV++ R L  
Sbjct: 373 IAVLQDRFVKYGFVEEKQIAKACKAMSDTLRVKTPSLEETVENLSGGNQQKVLIGRWLLT 432

Query: 432 QPRVLILDEPTRGVDIGAKSEIYRLINALAQSGVAILMISSELPEVVGLCDRVLVMREGT 491
            P++LILDEPTRG+D+GAK+EI+RLI+ LA++GVA++MISSE+PEV+G+ DR++VM EG 
Sbjct: 433 NPKILILDEPTRGIDVGAKAEIHRLISQLAKTGVAVIMISSEMPEVLGMSDRIMVMHEGR 492

Query: 492 LAGEVRPAGSAAETQERIIALAT 514
           + G +     A  TQ +++ LA+
Sbjct: 493 VTGFL---DRAEATQVKVMELAS 512


Lambda     K      H
   0.320    0.136    0.382 

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: 581
Number of extensions: 35
Number of successful extensions: 8
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: 540
Length of database: 513
Length adjustment: 35
Effective length of query: 505
Effective length of database: 478
Effective search space:   241390
Effective search space used:   241390
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: 52 (24.6 bits)

This GapMind analysis is from Sep 24 2021. 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