GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braD in Azospirillum brasilense Sp245

Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate AZOBR_RS25470 AZOBR_RS25470 ABC transporter permease

Query= uniprot:Q1MCU0
         (300 letters)



>FitnessBrowser__azobra:AZOBR_RS25470
          Length = 297

 Score =  169 bits (427), Expect = 9e-47
 Identities = 104/294 (35%), Positives = 162/294 (55%), Gaps = 17/294 (5%)

Query: 6   QQLLNGLTLGSIYGLVAIGYTMVYGIIGMINFAHGDIFMLGGFAALIVFLVLTSIFAGLP 65
           QQ++NG+ +GS Y L A+G+T+++G++ ++N AHG +FM G F  L     L     GLP
Sbjct: 4   QQIVNGIVVGSTYALFALGFTLIFGVLHVLNLAHGAVFMWGAFTGLFAVTAL-----GLP 58

Query: 66  VAVLLLVMLVVAMLMTSLWNWTIERVAYRPLR--GSFRLAPLITAIGMSITLSNFIQVTQ 123
               L     VAML   L +  ++ VA+RPLR  GS   A +I+++G++  L +  Q+  
Sbjct: 59  ----LPAAFAVAMLAAGLLSVLVDAVAFRPLRRRGSPEFAAIISSLGVAQILMSAAQIAS 114

Query: 124 GPRNKPIP----PMVSSVYQFGNISVSLKQIIIIVITAVLLTIFWYIVNRTALGRAQRAT 179
             + +  P    P+V   YQ   + VSL+QI+I+   AVL+      +  T+ GR  RA 
Sbjct: 115 NTQVQRFPFGTFPIV--FYQVFGLRVSLQQIVIVGSVAVLVAALLAFLFATSFGRQIRAV 172

Query: 180 EQDRKMAALLGVNVDQTISITFVMGAALAAVAGTMYLMYYGVASFNDGFTPGVKAFTAAV 239
               + A+LLGVN     ++TF +  ALA  AG +  + +    F  G    ++ F   V
Sbjct: 173 AISERTASLLGVNPGAVHALTFFLCGALAGAAGVIIGIAFNSVHFLMGEPYLLRGFVVIV 232

Query: 240 LGGIGSLPGAVFGGLLIGLIESLWSAYFTIAYKDVATFAILAFVLIFKPTGILG 293
           LGG+GS+ GAV GGLL G+I++L  A+ + A  D   F +L  +L+ +P+G  G
Sbjct: 233 LGGLGSVAGAVVGGLLFGMIQTLSVAFLSSALSDAILFGLLFVILLLRPSGFFG 286


Lambda     K      H
   0.329    0.143    0.421 

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: 284
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: 300
Length of database: 297
Length adjustment: 27
Effective length of query: 273
Effective length of database: 270
Effective search space:    73710
Effective search space used:    73710
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 48 (23.1 bits)

This GapMind analysis is from Sep 17 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