GapMind for catabolism of small carbon sources

 

Alignments for a candidate for atoB in Frischella perrara PEB0191

Align acetyl-CoA C-acetyltransferase [EC: 2.3.1.9] (characterized)
to candidate WP_039103927.1 FPB0191_RS02985 acetyl-CoA C-acetyltransferase

Query= reanno::pseudo5_N2C3_1:AO356_21640
         (393 letters)



>NCBI__GCF_000807275.1:WP_039103927.1
          Length = 391

 Score =  433 bits (1114), Expect = e-126
 Identities = 213/392 (54%), Positives = 295/392 (75%), Gaps = 2/392 (0%)

Query: 1   MQEVVIVAATRTAIGSFQGSLAAIPAPELGAAVIRRLLEQTGLSGEQVDEVILGQVLTAG 60
           M+E+VIVAA RTAIG F G+ + + A ELGA +I+ +L+++ +  +++D+VI+GQVLTAG
Sbjct: 1   MEEIVIVAAKRTAIGGFLGAFSELSATELGAMLIKYMLDESNIPVDEIDQVIMGQVLTAG 60

Query: 61  SGQNPARQASILAGLPHAVPALTLNKVCGSGLKALHLGAQAIRCGDAEVIIAGGMENMSL 120
            GQNPARQ ++ AGLP  V  LT+NKVCGSGL A++L  QAIR GDA++IIAGG E+MS 
Sbjct: 61  CGQNPARQTALKAGLPERVTGLTVNKVCGSGLVAINLAVQAIRNGDAQMIIAGGQESMST 120

Query: 121 APYVLPAARTGLRMGHAKMIDSMITDGLWDAFNDYHMGITAENLVDKYGISREEQDAFAA 180
           A +VL   R G R+GH +++D+++ DGL DAFN YHMGITAEN+ +++ ISREEQD+FA 
Sbjct: 121 AAHVLKKGRKGNRLGHLELVDTLLYDGLTDAFNQYHMGITAENIAEEFNISREEQDSFAL 180

Query: 181 ASQQKAVAAIEGGRFADEITPILIPQRKGDPVAFATDEQPRAGTTAESLGKLKPAFKKDG 240
           +SQ KA+ AI+   F+ EI PI +  +KG+ +    DE PR  T+   L  L+P FKKDG
Sbjct: 181 SSQNKALKAIQNSAFSSEIMPIKLTTKKGE-IVIDKDESPRE-TSFNKLSTLQPVFKKDG 238

Query: 241 SVTAGNASSLNDGAAAVILMSAEKAKALGLPVLAKISAYANAGVDPAIMGIGPVSATRRC 300
            VTAGN+S +NDGAAAVI+ S  +A +LGL  L  I+A+AN G++PA+MG+G +SA + C
Sbjct: 239 VVTAGNSSPINDGAAAVIICSKSRAISLGLKPLVSITAFANTGINPAMMGLGSISAIQAC 298

Query: 301 LDKAGWSLEQLDLIEANEAFAAQSLAVARELKWDMDKVNVNGGAIALGHPIGASGCRVLV 360
           L+K G S+  +DL E NEAFA+Q++A  + L    +K+NVNGGAIALGHPIGASGCR+LV
Sbjct: 299 LEKTGQSINDIDLFECNEAFASQAIATQKTLNLPDEKLNVNGGAIALGHPIGASGCRILV 358

Query: 361 SLLHEMIKRDAKKGLATLCIGGGQGVALALER 392
           SL++++  +    G+A LC+GGG+GVA+++ R
Sbjct: 359 SLIYQLFSKKLSTGIAALCVGGGEGVAMSIIR 390


Lambda     K      H
   0.317    0.133    0.376 

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: 464
Number of extensions: 12
Number of successful extensions: 2
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: 393
Length of database: 391
Length adjustment: 31
Effective length of query: 362
Effective length of database: 360
Effective search space:   130320
Effective search space used:   130320
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 24 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