GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pimB in Pseudomonas simiae WCS417

Align 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized)
to candidate GFF1320 PS417_06710 beta-ketoadipyl CoA thiolase

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



>FitnessBrowser__WCS417:GFF1320
          Length = 400

 Score =  243 bits (619), Expect = 9e-69
 Identities = 162/407 (39%), Positives = 220/407 (54%), Gaps = 32/407 (7%)

Query: 1   MTEAVIVSTARTPIGKAYRGALNATEGATLLGHAIEHAVKR-AGIDPKEVEDVVMGAAMQ 59
           M +  I    RTPIG+ + G L+      L    I+  ++R   +D   V++V +G A Q
Sbjct: 1   MRDVFICDAIRTPIGR-FGGGLSTVRADDLAALPIKALIERNPSVDWTAVDEVFLGCANQ 59

Query: 60  QGATGGNIARKALLRAGLPVTTAGTTIDRQCASGLQAIALAARSVLFDGVEIAVGGGGES 119
            G    N+AR ALL AGLP +  G T++R CASG+ AI  A R++    +E+A+ GG ES
Sbjct: 60  AGEDNRNVARMALLLAGLPESIPGVTLNRLCASGMDAIGTAFRAIASGEMELAIAGGVES 119

Query: 120 IS----------------LVQNDKMNTFHAVDPALEAIKGDVYMAMLDTAETVAKRYGIS 163
           +S                +   D    +  ++P ++A  G    AM  TA+ VA  Y +S
Sbjct: 120 MSRAPFVMGKADAAFSRTMKLEDTTIGWRFINPLMKAQYG--VDAMPQTADNVADDYHVS 177

Query: 164 RERQDEYSLESQRRTAAAQQGGKFNDEIAPISTKMGVVDKATGAVSFKDITLSQDEGPRP 223
           R  QD ++L SQ+RTAAAQ  G F +EI P+            A    +  + QDE PR 
Sbjct: 178 RADQDAFALRSQQRTAAAQAAGFFAEEIVPVRV----------AHKKGETVVEQDEHPRA 227

Query: 224 ETTAEGLAGLKAVRGEGFTITAGNASQLSDGASATVIMSDKTAAAKGLKPLGIFRGMVSY 283
           +TT E L  LK V G   T+TAGNAS ++DGA+A ++ S +     GL       GM S 
Sbjct: 228 DTTLEALTKLKPVNGPDKTVTAGNASGVNDGAAALILASAEAVKKHGLTARARVLGMASA 287

Query: 284 GCEPDEMGIGPVFAVPRLLKRHGLSVDDIGLWELNEAFAVQVLYCRDKLGI--DPEKLNV 341
           G  P  MGIGPV AV +L++R GL+V D  + ELNEAFA Q L    +LGI  D  ++N 
Sbjct: 288 GVAPRVMGIGPVPAVRKLVERLGLAVTDFDVIELNEAFASQGLAVLRELGIADDAPQVNP 347

Query: 342 NGGAISVGHPYGMSGARLAGHALIEGRRRKAKYAVVTMCVGGGMGSA 388
           NGGAI++GHP GMSGARL   AL +  +      + TMCVG G G A
Sbjct: 348 NGGAIALGHPLGMSGARLVLTALHQLEKTGGSKGLATMCVGVGQGLA 394


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: 414
Number of extensions: 23
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