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 3610436 Dshi_3817 beta-ketoadipyl CoA thiolase (RefSeq)

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



>FitnessBrowser__Dino:3610436
          Length = 400

 Score =  261 bits (667), Expect = 2e-74
 Identities = 172/411 (41%), Positives = 226/411 (54%), Gaps = 31/411 (7%)

Query: 3   EAVIVSTARTPIGKAYRGALNATEGATLLGHAIEHAVKR-AGIDPKEVEDVVMGAAMQQG 61
           +AVI    RTPIG+ Y GAL++     L    I   + R  G+D   V++V+ GAA Q G
Sbjct: 2   DAVICDGVRTPIGR-YGGALSSVRADDLAALPIAALMARNPGVDWARVDEVIYGAANQAG 60

Query: 62  ATGGNIARKALLRAGLPVTTAGTTIDRQCASGLQAIALAARSVLFDGVEIAVGGGGESIS 121
               N+AR A L AGLP    G T++R CASG+ A+  AAR +     ++A+ GG ES+S
Sbjct: 61  EDNRNVARMAALLAGLPEEVPGLTVNRLCASGMDAVGAAARGIKAGEYDLAIAGGIESMS 120

Query: 122 LVQ----------------NDKMNTFHAVDPALEAIKGDVYMAMLDTAETVAKRYGISRE 165
                              +D    +  V+P + A+ G     M  TA+TVA  Y ISR 
Sbjct: 121 RAPFVMPKAESAFTRAATVHDTTIGWRFVNPKIAAMHG--IDTMPQTADTVAAAYEISRA 178

Query: 166 RQDEYSLESQRRTAAAQQGGKFNDEIAPISTKMGVVDKATGAVSFKDITLSQDEGPRPET 225
            QD ++  SQ R AAA   G F DEI P+                  I + +DE PRP T
Sbjct: 179 DQDAFAARSQARWAAADAAGLFADEIVPVPVPQR---------GSAPILVDRDEHPRPGT 229

Query: 226 TAEGLAGLKAVRGEGFTITAGNASQLSDGASATVIMSDKTAAAKGLKPLGIFRGMVSYGC 285
            A  LAGLK + G G ++TAGNAS ++DGA+A +I S   A A GL P+    GM S G 
Sbjct: 230 DAARLAGLKGINGPGLSVTAGNASGVNDGAAALLIASAAAARAHGLTPMARVVGMASAGV 289

Query: 286 EPDEMGIGPVFAVPRLLKRHGLSVDDIGLWELNEAFAVQVLYCRDKLGI--DPEKLNVNG 343
            P  MGIGPV A  +LL R GL++D + + ELNEAFA Q L    +LG+  D  ++N NG
Sbjct: 290 APRVMGIGPVPASRKLLDRAGLTLDQMDVIELNEAFASQSLATLRQLGLADDDVRVNPNG 349

Query: 344 GAISVGHPYGMSGARLAGHALIEGRRRKAKYAVVTMCVGGGMGSAGLFEIV 394
           GAI++GHP GMSGARL   A  + RR   +YA+ TMCVG G G+A + E V
Sbjct: 350 GAIAMGHPLGMSGARLVLTAAHQLRRTGGRYALCTMCVGVGQGTALILERV 400


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: 438
Number of extensions: 32
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: 400
Length adjustment: 31
Effective length of query: 364
Effective length of database: 369
Effective search space:   134316
Effective search space used:   134316
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