GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pimB in Sinorhizobium fredii NGR234

Align 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized)
to candidate WP_012709751.1 NGR_RS27475 acetyl-CoA C-acetyltransferase

Query= metacyc::MONOMER-20679
         (395 letters)



>NCBI__GCF_000018545.1:WP_012709751.1
          Length = 393

 Score =  252 bits (644), Expect = 1e-71
 Identities = 150/395 (37%), Positives = 224/395 (56%), Gaps = 25/395 (6%)

Query: 5   VIVSTARTPIGKAYRGALNATEGATLLGHAIEHAVKRAGIDPKEVEDVVMGAAMQQGATG 64
           VI S ART +G ++ GA   T    L    I+  ++RAG+D  EV++V++G  +  G  G
Sbjct: 7   VIASAARTAVG-SFNGAFGNTPAHELGATVIKAVLERAGVDAAEVDEVILGQVLPAGE-G 64

Query: 65  GNIARKALLRAGLPVTTAGTTIDRQCASGLQAIALAARSVLFDGVEIAVGGGGESISLVQ 124
            N AR+A ++AG+P       +++ C SGL+A+AL  + +      I V GG ES+S+  
Sbjct: 65  QNPARQAAIKAGVPQEKTAWGMNQLCGSGLRAVALGMQQIATGDASIIVAGGMESMSMAP 124

Query: 125 ND-------KMNTFHAVDPALEAIKGDVYMA--MLDTAETVAKRYGISRERQDEYSLESQ 175
           +        KM  +  +D  ++    D +    M  TAE VA+++ ++RE QDE++L SQ
Sbjct: 125 HCAHLRGGVKMGDYKMIDTMIKDGLTDAFYGYHMGTTAENVARKWQLTREEQDEFALRSQ 184

Query: 176 RRTAAAQQGGKFNDEIAP--ISTKMGVVDKATGAVSFKDITLSQDEGPRPETTAEGLAGL 233
            +  AAQ+ G+F DEI P  + T+ G            D+T+ QDE  R   T E +A L
Sbjct: 185 NKAEAAQKAGRFADEIVPFIVKTRKG------------DVTVDQDEYIRHGATLESIAKL 232

Query: 234 KAVRGEGFTITAGNASQLSDGASATVIMSDKTAAAKGLKPLGIFRGMVSYGCEPDEMGIG 293
           +    +  T+TAGNAS L+DGA+AT++M++  AA +G++PL       + G +P  MG G
Sbjct: 233 RPAFDKEGTVTAGNASGLNDGAAATLLMTEAEAAKRGIQPLARIVSWATAGVDPQIMGTG 292

Query: 294 PVFAVPRLLKRHGLSVDDIGLWELNEAFAVQVLYCRDKLGIDPEKLNVNGGAISVGHPYG 353
           P+ A  + L++ G  + D+ L E NEAFA Q       LG DP  +NVNGGAI++GHP G
Sbjct: 293 PIPASRKALEKAGWPIGDVELVEANEAFAAQACAVNKDLGWDPSIVNVNGGAIAIGHPIG 352

Query: 354 MSGARLAGHALIEGRRRKAKYAVVTMCVGGGMGSA 388
            SGAR+    L E +RR     + T+C+GGGMG A
Sbjct: 353 ASGARVLNTLLFEMKRRGVSKGLATLCIGGGMGVA 387


Lambda     K      H
   0.316    0.134    0.378 

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: 427
Number of extensions: 21
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 395
Length of database: 393
Length adjustment: 31
Effective length of query: 364
Effective length of database: 362
Effective search space:   131768
Effective search space used:   131768
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Apr 09 2024. 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