GapMind for catabolism of small carbon sources

 

Aligments for a candidate for pimB in Sinorhizobium meliloti 1021

Align 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized)
to candidate SMc03879 SMc03879 acetyl-CoA acetyltransferase

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



>lcl|FitnessBrowser__Smeli:SMc03879 SMc03879 acetyl-CoA
           acetyltransferase
          Length = 393

 Score =  248 bits (634), Expect = 2e-70
 Identities = 150/395 (37%), Positives = 225/395 (56%), Gaps = 25/395 (6%)

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

Query: 65  GNIARKALLRAGLPVTTAGTTIDRQCASGLQAIALAARSVLFDGVEIAVGGGGESISLVQ 124
            N AR+A ++AGLP       +++ C SGL+A+AL  + +     ++ V GG ES+S+  
Sbjct: 65  QNPARQAAMKAGLPQEKTAWGMNQLCGSGLRAVALGMQQIATGDAKVIVAGGMESMSMAP 124

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

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

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

Query: 294 PVFAVPRLLKRHGLSVDDIGLWELNEAFAVQVLYCRDKLGIDPEKLNVNGGAISVGHPYG 353
           P+ A  + L++ G SV DI L E NEAFA Q       LG DP  +NVNGGAI++GHP G
Sbjct: 293 PIPASRKALEKAGWSVADIELVEANEAFAAQACAVNKDLGWDPSIVNVNGGAIAIGHPIG 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: 425
Number of extensions: 23
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 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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