GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pimB in Nocardioides daejeonensis MJ31

Align 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized)
to candidate WP_110206636.1 DNK54_RS08955 thiolase family protein

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



>NCBI__GCF_003194585.1:WP_110206636.1
          Length = 392

 Score =  242 bits (617), Expect = 2e-68
 Identities = 156/399 (39%), Positives = 218/399 (54%), Gaps = 26/399 (6%)

Query: 5   VIVSTARTPIGKAYRGALNATEGATLLGHAIEHAVKRAGIDPKEVEDVVMGAAMQQGATG 64
           VIV  ARTPIG ++ G L       L   A+  A+ RAG+  +++ +VVMG   Q G   
Sbjct: 7   VIVDGARTPIG-SFGGVLKDVPAHELGAVAVTEALSRAGVRGEQIREVVMGQIGQVGPDA 65

Query: 65  GNIARKALLRAGLPVTTAGTTIDRQCASGLQAIALAARSVLFDGVEIAVGGGGESIS--- 121
            N AR+  L AGLP +    T++R C SGLQAI  AA  + ++ ++ A+GGG ES+S   
Sbjct: 66  YN-ARRVALAAGLPQSVPAYTVNRLCGSGLQAIWSAAMEMRWNNLDFAIGGGDESMSRMP 124

Query: 122 LVQNDKMNTFHAVDPALEAIKGDVYMA--------MLDTAETVAKRYGISRERQDEYSLE 173
            +     N +   D AL  + G V M         M  TAE VA +YG+ R +QDE+++E
Sbjct: 125 FLDFGARNGYKLGDRAL--VDGTVGMLTDPFSNKHMGVTAENVAAKYGVDRVQQDEFAVE 182

Query: 174 SQRRTAAAQQGGKFNDEIAPISTKMGVVDKATGAVSFKDITLSQDEGPRPETTAEGLAGL 233
           SQRR A  +    F +EI P+                K  T+  DE P+P TT E L  L
Sbjct: 183 SQRRAATDEAKAAFAEEIVPVEV-----------AGRKPYTVEVDEHPKPGTTMETLGKL 231

Query: 234 KAVRGEGFTITAGNASQLSDGASATVIMSDKTAAAKGLKPLGIFRGMVSYGCEPDEMGIG 293
           +A   +  ++TAGNAS ++DGA A V+ ++  AA  GL PL     + +   EP+ MG  
Sbjct: 232 RAAFVKDGSVTAGNASGINDGAGAVVLATEAAAAEHGLSPLVSIEAVSTGAMEPELMGYA 291

Query: 294 PVFAVPRLLKRHGLSVDDIGLWELNEAFAVQVLYCRDKLGIDPEKLNVNGGAISVGHPYG 353
           PV A+  L +R GL+  DIG  ELNEAFA Q +      G+DP ++N  GGAI++GHP G
Sbjct: 292 PVLALKDLFERTGLTPKDIGTIELNEAFASQAVAVSRDAGLDPAQVNPYGGAIALGHPVG 351

Query: 354 MSGARLAGHALIEGRRRKAKYAVVTMCVGGGMGSAGLFE 392
            +GA L+  A     R   ++ +VTMC+GGG   A LF+
Sbjct: 352 ATGAILSVRAAKTMVRNDLEFGIVTMCIGGGQALAALFK 390


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: 446
Number of extensions: 29
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: 395
Length of database: 392
Length adjustment: 31
Effective length of query: 364
Effective length of database: 361
Effective search space:   131404
Effective search space used:   131404
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 24 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