GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ac3H11_1695 in Azospirillum thiophilum BV-S

Align ABC transporter permease (characterized, see rationale)
to candidate WP_045583514.1 AL072_RS26405 branched-chain amino acid ABC transporter permease

Query= uniprot:A0A165KC95
         (309 letters)



>NCBI__GCF_001305595.1:WP_045583514.1
          Length = 301

 Score =  260 bits (665), Expect = 2e-74
 Identities = 141/307 (45%), Positives = 201/307 (65%), Gaps = 18/307 (5%)

Query: 1   MDILLQQIINGLVLGSMYALIALGYTMVYGIIQLINFAHGEVLMIGALTSWSCIGMMQGA 60
           MD  +QQ+INGL LG++Y LIA+GYTMVYGII +INFAHGE+ MIGA      + ++   
Sbjct: 1   MDYFIQQLINGLSLGAIYGLIAIGYTMVYGIIGMINFAHGEIYMIGAF-----VALITFL 55

Query: 61  MPGAPG--WV--ILLLATIIACVVAATLNFVIEKVAYRPLRSSPRLAPLITAIGMSILLQ 116
             GA G  WV   LL+  + + +  +   + +E++AYRPLRSSPRLAPLI+AIGMSI LQ
Sbjct: 56  AIGALGITWVPLALLIMLVASMLFTSVYGWTVERIAYRPLRSSPRLAPLISAIGMSIFLQ 115

Query: 117 TLAMIIWKPNYKPYPTMLPSSPFEIGGAF-ITPTQILILGVTAVALASLVYLVNHTNLGR 175
               I+     KP   +LP +   + GA  ++  ++  + +T V +     L+N T+LGR
Sbjct: 116 NYIQILQGARSKPLQPILPGNLTLMDGAVSVSYVRLATIVITLVLMVGFTILINRTSLGR 175

Query: 176 AMRATAENPRVASLMGVKPDMVISATFIIGAVLAAIAGIMYASNYGTAQHTMGFLPGLKA 235
           A RA  ++ ++A L+GV  D VIS TF++GA LAA+AG+M    YG     +GFL G+K+
Sbjct: 176 AQRACEQDKKMAGLLGVNVDRVISLTFVMGAALAAVAGMMVLLIYGVIDFYIGFLAGVKS 235

Query: 236 FTAAVFGGIGNLAGAVVGGILLGLIEAIGSGYIGTLTGGLLGSHYTDIFAFIVLIIILTL 295
           FTAAV GG+G+L GA++GG+++GLIEA  SGY+        GS + D+  F +L+++L  
Sbjct: 236 FTAAVLGGVGSLPGAMLGGVVIGLIEAFWSGYV--------GSEWKDVATFSILVLVLIF 287

Query: 296 RPSGLLG 302
           RP+GLLG
Sbjct: 288 RPTGLLG 294


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: 291
Number of extensions: 17
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: 301
Length adjustment: 27
Effective length of query: 282
Effective length of database: 274
Effective search space:    77268
Effective search space used:    77268
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 24 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