GapMind for catabolism of small carbon sources

 

Alignments for a candidate for atoB in Pseudomonas fluorescens GW456-L13

Align acetyl-CoA C-acetyltransferase (EC 2.3.1.9) (characterized)
to candidate PfGW456L13_3394 3-ketoacyl-CoA thiolase (EC 2.3.1.16) @ Acetyl-CoA acetyltransferase (EC 2.3.1.9)

Query= BRENDA::Q0KAI3
         (392 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3394
          Length = 391

 Score =  358 bits (919), Expect = e-103
 Identities = 211/403 (52%), Positives = 262/403 (65%), Gaps = 24/403 (5%)

Query: 1   MQQAVIVDAIRSPMGRSKPGSAFTELHATELLAQVIKGLVERNKLDPGLVDDVITGCVTQ 60
           M+  VIVDA+R+P+G+ +   + + + A  L + VI  L+ER  + P LVDDVI G VTQ
Sbjct: 1   MKDIVIVDAVRTPIGKFR--GSLSGVRADHLGSLVISRLLERVDVSPTLVDDVIFGNVTQ 58

Query: 61  AGEQSAGPGRVAWLAAGFPDHVPATTIDRKCGSSQQAVHFAAQGIMAGAYDIVIACGIES 120
            GEQSA   R A L AG+P  V   TIDRKCGS + AVH A   I AGA DIV+A G E+
Sbjct: 59  IGEQSANIARTALLGAGWPVTVAGLTIDRKCGSGEVAVHMAVGAIAAGAADIVVAGGAEN 118

Query: 121 MSRVPMGSAR-IGQNPYGPSMEARYAPGLVSQGVAAELVAAKYELSRHDMDSYSARSHEL 179
           MSRVPMGS R I    +G     RY   L SQG AAE +A K+ LSR  +D ++  SH+ 
Sbjct: 119 MSRVPMGSNREIHGAAFGWMAAQRYE--LTSQGEAAERMADKWALSRDALDDFAFASHQR 176

Query: 180 AATARESGAFRREILGI----------STPNGLVEQDETIRPGTSVEKLGTLQASFRNDE 229
           AA A ++G F  E + +          S P G++  DETIR  TS EKL TL+ SFR D 
Sbjct: 177 AAAACDAGYFDNETIPVVVEELREKELSEPAGVLRHDETIRRDTSREKLSTLKTSFRPDT 236

Query: 230 LSARFPQIGWNVTAGNASQISDGASAMLLMSESMAQRLGLKPRARFVAFDVCGDDPVMML 289
                      +TAGN+SQISDGA+A+LLMS   A++LGLK RAR VAF   G DP +ML
Sbjct: 237 ---------GRITAGNSSQISDGAAALLLMSADTAKKLGLKARARVVAFTTVGSDPTLML 287

Query: 290 TAPIPASQRAIKKSGLKLDQIDHYEINEAFACVPLAWQRALGADPARLNPRGGAIALGHP 349
           T PI A+Q+ + K+GL ++ ID +E+NEAFA VPLAW +  G   ++LN  GGAIALGHP
Sbjct: 288 TGPIAATQKVLAKAGLSINDIDLFEVNEAFASVPLAWMQETGVPHSKLNVNGGAIALGHP 347

Query: 350 LGASGVRLMTTMLHALEDSGQRYGLQSMCEAGGMANATIIERL 392
           LGASG RLMTTML+ LE  G RYGLQ++C AGGM  ATIIERL
Sbjct: 348 LGASGARLMTTMLNELERRGGRYGLQAICCAGGMGTATIIERL 390


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: 411
Number of extensions: 12
Number of successful extensions: 5
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: 391
Length adjustment: 31
Effective length of query: 361
Effective length of database: 360
Effective search space:   129960
Effective search space used:   129960
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