GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pimB in Dinoroseobacter shibae DFL-12

Align 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized)
to candidate 3609683 Dshi_3066 acetyl-CoA acetyltransferase (RefSeq)

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



>FitnessBrowser__Dino:3609683
          Length = 391

 Score =  247 bits (631), Expect = 4e-70
 Identities = 150/399 (37%), Positives = 221/399 (55%), Gaps = 25/399 (6%)

Query: 1   MTEAVIVSTARTPIGKAYRGALNATEGATLLGHAIEHAVKRAGIDPKEVEDVVMGAAMQQ 60
           MT  VI S ART +G ++ G+   T    L    +E  V RAGI+  EV + ++G  +  
Sbjct: 1   MTNVVIASAARTAVG-SFGGSFANTPAHDLGSAVLEALVARAGIEKGEVSETILGQVLT- 58

Query: 61  GATGGNIARKALLRAGLPVTTAGTTIDRQCASGLQAIALAARSVLFDGVEIAVGGGGESI 120
           G  G N AR+A + AGLP  +A   +++ C SGL+A+AL A+ +     EI   GG E++
Sbjct: 59  GGQGQNPARQAHINAGLPQESAAWGLNQVCGSGLRAVALGAQHIQLGDAEIVCAGGQENM 118

Query: 121 SLVQN-------DKMNTFHAVDPALEAIKGDVYMA--MLDTAETVAKRYGISRERQDEYS 171
           +L  +        KM     +D  +     D +    M  TAE VA+++ ISRE QDE++
Sbjct: 119 TLSPHVANLRAGQKMGDMKFIDSMIRDGLWDAFNGYHMGQTAENVAEKWQISREMQDEFA 178

Query: 172 LESQRRTAAAQQGGKFNDEIAP--ISTKMGVVDKATGAVSFKDITLSQDEGPRPETTAEG 229
           + SQ +  AAQ+ GKF+DE+    I T+ G            DI + +DE  R   T E 
Sbjct: 179 VASQNKAEAAQKAGKFDDEVVAFTIKTRKG------------DIVVDKDEYIRHGATMEA 226

Query: 230 LAGLKAVRGEGFTITAGNASQLSDGASATVIMSDKTAAAKGLKPLGIFRGMVSYGCEPDE 289
           +  L+    +  ++TA NAS L+DGA+  ++MS + A  +G+ P+       + G +P  
Sbjct: 227 MQKLRPAFTKDGSVTAANASGLNDGAAGVLLMSAENAEKRGITPMARIASYATAGLDPSI 286

Query: 290 MGIGPVFAVPRLLKRHGLSVDDIGLWELNEAFAVQVLYCRDKLGIDPEKLNVNGGAISVG 349
           MG+GP++A  + L++ G  VDD+ L E NEAFA Q       +G DP  +NVNGGAI++G
Sbjct: 287 MGVGPIYASRKALEKAGWKVDDLDLVEANEAFAAQACAVNKDMGWDPAIVNVNGGAIAIG 346

Query: 350 HPYGMSGARLAGHALIEGRRRKAKYAVVTMCVGGGMGSA 388
           HP G SGAR+    L E +RR AK  + T+C+GGGMG A
Sbjct: 347 HPIGASGARVLNTLLFEMQRRDAKKGLATLCIGGGMGVA 385


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: 398
Number of extensions: 12
Number of successful extensions: 3
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: 391
Length adjustment: 31
Effective length of query: 364
Effective length of database: 360
Effective search space:   131040
Effective search space used:   131040
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:

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