GapMind for catabolism of small carbon sources

 

Alignments for a candidate for atoB in Herbaspirillum seropedicae SmR1

Align acetyl-CoA:acetyl-CoA C-acetyltransferase / acetyl-CoA:propanoyl-CoA 2-C-acetyltransferase (EC 2.3.1.9; EC 2.3.1.16) (characterized)
to candidate HSERO_RS04635 HSERO_RS04635 acetyl-CoA acetyltransferase

Query= reanno::pseudo3_N2E3:AO353_25685
         (397 letters)



>FitnessBrowser__HerbieS:HSERO_RS04635
          Length = 400

 Score =  484 bits (1247), Expect = e-141
 Identities = 251/398 (63%), Positives = 302/398 (75%), Gaps = 6/398 (1%)

Query: 3   MSHDPIVIVSAVRTPMGGFQGELKSLSAPQLGAAAIRAAVERAGVAADAV---EEVLFGC 59
           MS DP+VIVSA RT MG FQG L  L AP LGA AI AA++RA ++A  +   E+V  GC
Sbjct: 1   MSEDPVVIVSAARTAMGSFQGALADLPAPHLGAVAISAALQRAQLSAAQIAQIEQVWMGC 60

Query: 60  VLSAGLGQAPARQAALGAGLDKSTRCTTLNKMCGSGMEAAILAHDMLLAGSADVVVAGGM 119
           VL AGLGQAPARQAAL AGL ++  C TLNK+CGS M+A +L HD +LAGSA +VVAGGM
Sbjct: 61  VLQAGLGQAPARQAALRAGLPQTVACATLNKVCGSAMQAVMLGHDSILAGSASMVVAGGM 120

Query: 120 ESMSNAPYLLDRARSGYRMGHGKVLDHMFLDGLEDAYD---KGRLMGTFAEDCAEANGFT 176
           ESMSNAPYLL +AR GYR+GH ++LDHMFLDGLEDAY    +GRLMGTFAEDCA   GFT
Sbjct: 121 ESMSNAPYLLPKARRGYRLGHDRLLDHMFLDGLEDAYSDQYRGRLMGTFAEDCASEFGFT 180

Query: 177 REAQDEFAIASTTRAQQAIKDGSFNAEIVPLQVIVGKEQKLITDDEQPPKAKLDKIASLK 236
           R  QD FA+ ST RA+QAI  G F+ E+VP+ V   K   +I+ DE P    L++IA+LK
Sbjct: 181 RAQQDAFAVQSTLRARQAISGGGFDWEVVPVDVAGKKGSVVISQDEGPMAVNLERIATLK 240

Query: 237 PAFRDGGTVTAANSSSISDGAAALLLMRRSEAEKRGLKPLAVIHGHAAFADTPGLFPVAP 296
           PAF   GTVTAANSSSISDGAAALLLMR S A K+GL PLA I GHA++A  P  FP AP
Sbjct: 241 PAFSVDGTVTAANSSSISDGAAALLLMRESAALKQGLTPLARILGHASYAGAPEKFPTAP 300

Query: 297 VGAIKKLLKKTGWSLDEVELFEVNEAFAVVSLVTMTKLEIPHSKVNVHGGACALGHPIGA 356
           +G ++K+  KTG      +LFE+NEAFAVV +    +L+I   K+NVHGGACALGHPIGA
Sbjct: 301 IGVLRKIFAKTGLDAASTDLFEINEAFAVVPMAASRELDIDMEKINVHGGACALGHPIGA 360

Query: 357 SGARILVTLLSALRQKGLKRGVAAICIGGGEATAMAVE 394
           SGARI+V+LL AL+ +GLK G+A++CIGGGEATA+A+E
Sbjct: 361 SGARIIVSLLGALKARGLKTGIASLCIGGGEATAIALE 398


Lambda     K      H
   0.318    0.133    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: 482
Number of extensions: 15
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: 397
Length of database: 400
Length adjustment: 31
Effective length of query: 366
Effective length of database: 369
Effective search space:   135054
Effective search space used:   135054
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