GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ac3H11_1695 in Azospirillum brasilense Sp245

Align ABC transporter permease (characterized, see rationale)
to candidate AZOBR_RS25470 AZOBR_RS25470 ABC transporter permease

Query= uniprot:A0A165KC95
         (309 letters)



>FitnessBrowser__azobra:AZOBR_RS25470
          Length = 297

 Score =  183 bits (464), Expect = 5e-51
 Identities = 111/303 (36%), Positives = 174/303 (57%), Gaps = 20/303 (6%)

Query: 3   ILLQQIINGLVLGSMYALIALGYTMVYGIIQLINFAHGEVLMIGALTSWSCIGMMQGAMP 62
           ++ QQI+NG+V+GS YAL ALG+T+++G++ ++N AHG V M GA T     G+      
Sbjct: 1   LVAQQIVNGIVVGSTYALFALGFTLIFGVLHVLNLAHGAVFMWGAFT-----GLFAVTAL 55

Query: 63  GAPGWVILLLATIIACVVAATLNFVIEKVAYRPLR--SSPRLAPLITAIGMSILLQTLAM 120
           G P    L  A  +A + A  L+ +++ VA+RPLR   SP  A +I+++G++ +L + A 
Sbjct: 56  GLP----LPAAFAVAMLAAGLLSVLVDAVAFRPLRRRGSPEFAAIISSLGVAQILMSAAQ 111

Query: 121 IIWKPNYKPYPT-MLPSSPFEIGGAFITPTQILILGVTAVALASLVYLVNHTNLGRAMRA 179
           I      + +P    P   +++ G  ++  QI+I+G  AV +A+L+  +  T+ GR +RA
Sbjct: 112 IASNTQVQRFPFGTFPIVFYQVFGLRVSLQQIVIVGSVAVLVAALLAFLFATSFGRQIRA 171

Query: 180 TAENPRVASLMGVKPDMVISATFIIGAVLAAIAGIMYASNYGTAQHTMGFLPGLKAFTAA 239
            A + R ASL+GV P  V + TF +   LA  AG++    + +    MG    L+ F   
Sbjct: 172 VAISERTASLLGVNPGAVHALTFFLCGALAGAAGVIIGIAFNSVHFLMGEPYLLRGFVVI 231

Query: 240 VFGGIGNLAGAVVGGILLGLIEAIGSGYIGTLTGGLLGSHYTDIFAFIVLIIILTLRPSG 299
           V GG+G++AGAVVGG+L G+I+        TL+   L S  +D   F +L +IL LRPSG
Sbjct: 232 VLGGLGSVAGAVVGGLLFGMIQ--------TLSVAFLSSALSDAILFGLLFVILLLRPSG 283

Query: 300 LLG 302
             G
Sbjct: 284 FFG 286


Lambda     K      H
   0.327    0.142    0.419 

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: 187
Number of extensions: 9
Number of successful extensions: 4
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: 309
Length of database: 297
Length adjustment: 27
Effective length of query: 282
Effective length of database: 270
Effective search space:    76140
Effective search space used:    76140
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 (21.7 bits)
S2: 48 (23.1 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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