GapMind for catabolism of small carbon sources

 

Alignments for a candidate for atoB in Klebsiella michiganensis M5al

Align acetyl-CoA C-acetyltransferase (EC 2.3.1.9) (characterized)
to candidate BWI76_RS01360 BWI76_RS01360 acetyl-CoA C-acyltransferase FadA

Query= BRENDA::Q0KAI3
         (392 letters)



>FitnessBrowser__Koxy:BWI76_RS01360
          Length = 387

 Score =  283 bits (725), Expect = 5e-81
 Identities = 175/401 (43%), Positives = 238/401 (59%), Gaps = 23/401 (5%)

Query: 1   MQQAVIVDAIRSPMGRSKPGSAFTELHATELLAQVIKGLVERN-KLDPGLVDDVITGCVT 59
           M+Q VIVDA+R+PMGRSK G AF  + A +L A +++ L+ RN  L+   +DD+  GCV 
Sbjct: 1   MEQVVIVDAVRTPMGRSK-GGAFRHVRADDLSAHLMRSLLSRNPSLEASAIDDIYWGCVQ 59

Query: 60  QAGEQSAGPGRVAWLAAGFPDHVPATTIDRKCGSSQQAVHFAAQGIMAGAYDIVIACGIE 119
           Q  EQ     R A L A  P  VPATT++R CGSS QA+H AA+ IM G   + +  G+E
Sbjct: 60  QTLEQGFNIARNAALLAEIPHSVPATTVNRLCGSSMQALHDAARMIMTGDASVCLIGGVE 119

Query: 120 SMSRVPMGSARIGQNPYGPSMEARYAPGLVSQGVAAELVAAKYELSRHDMDSYSARSHEL 179
            M  VPM         + P +    A      G+ AE++A  + +SR   D ++ARSH  
Sbjct: 120 HMGHVPMSHGV----DFHPGLSRNVAKAAGMMGLTAEMLARLHGISREMQDQFAARSHAR 175

Query: 180 AATARESGAFRREIL--GISTPNGLVEQ---DETIRPGTSVEKLGTLQASFRNDELSARF 234
           A  A +SGAF+ EI+  G    +G+++    DE IRP T+VE L  L+ +F         
Sbjct: 176 AWAATQSGAFKTEIIPTGGHDADGVLKSYSYDEVIRPETTVEALAALRPAFD-------- 227

Query: 235 PQIGWNVTAGNASQISDGASAMLLMSESMAQRLGLKPRARFVAFDVCGDDPVMMLTAPIP 294
           P  G  VTAG +S +SDGA+AMLLMSES A+ LGLKPRAR  +  V G DP +M   P+P
Sbjct: 228 PVTG-TVTAGTSSALSDGAAAMLLMSESRARELGLKPRARVRSMAVVGCDPSIMGYGPVP 286

Query: 295 ASQRAIKKSGLKLDQIDHYEINEAFACVPLAWQRALG---ADPARLNPRGGAIALGHPLG 351
           AS+ A+KK+GL    ID +E+NEAFA   L   + LG       ++N  GGAIALGHPLG
Sbjct: 287 ASKLALKKAGLSASDIDVFEMNEAFAAQILPCIKDLGLMEQIDEKINLNGGAIALGHPLG 346

Query: 352 ASGVRLMTTMLHALEDSGQRYGLQSMCEAGGMANATIIERL 392
            SG R+ TT+++ +E    ++GL +MC   G   AT+ ER+
Sbjct: 347 CSGARISTTLINQMERKDAQFGLATMCIGLGQGIATVFERV 387


Lambda     K      H
   0.318    0.132    0.384 

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: 418
Number of extensions: 16
Number of successful extensions: 6
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: 392
Length of database: 387
Length adjustment: 30
Effective length of query: 362
Effective length of database: 357
Effective search space:   129234
Effective search space used:   129234
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 (21.7 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