GapMind for catabolism of small carbon sources

 

Alignments for a candidate for atoB in Escherichia coli BW25113

Align acetyl-CoA C-acetyltransferase [EC: 2.3.1.9] (characterized)
to candidate 16925 b2844 putative acyltransferase (VIMSS)

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



>FitnessBrowser__Keio:16925
          Length = 393

 Score =  523 bits (1347), Expect = e-153
 Identities = 256/392 (65%), Positives = 325/392 (82%), Gaps = 1/392 (0%)

Query: 1   MQEVVIVAATRTAIGSFQGSLAAIPAPELGAAVIRRLLEQTGLSGEQVDEVILGQVLTAG 60
           M++VVIV A RT IG F+G+LA   A ELG+ V++ L+E+TG+    VDEVILGQVLTAG
Sbjct: 1   MKDVVIVGALRTPIGCFRGALAGHSAVELGSLVVKALIERTGVPAYAVDEVILGQVLTAG 60

Query: 61  SGQNPARQASILAGLPHAVPALTLNKVCGSGLKALHLGAQAIRCGDAEVIIAGGMENMSL 120
           +GQNPARQ++I  GLP++V A+T+N VCGSGLKALHL  QAI+CG+A+++IAGG ENMS 
Sbjct: 61  AGQNPARQSAIKGGLPNSVSAITINDVCGSGLKALHLATQAIQCGEADIVIAGGQENMSR 120

Query: 121 APYVLPAARTGLRMGHAKMIDSMITDGLWDAFNDYHMGITAENLVDKYGISREEQDAFAA 180
           AP+VL  +RTG ++G+++++DS++ DGLWDAFNDYH+G+TAENL  +YGISR+ QDA+A 
Sbjct: 121 APHVLTDSRTGAQLGNSQLVDSLVHDGLWDAFNDYHIGVTAENLAREYGISRQLQDAYAL 180

Query: 181 ASQQKAVAAIEGGRFADEITPILIPQRKGDPVAFATDEQPRAGTTAESLGKLKPAFKKDG 240
           +SQQKA AAI+ GRF DEI P++  Q  G  +   TDEQPR   +AE L +L P+F   G
Sbjct: 181 SSQQKARAAIDAGRFKDEIVPVM-TQSNGQTLVVDTDEQPRTDASAEGLARLNPSFDSLG 239

Query: 241 SVTAGNASSLNDGAAAVILMSAEKAKALGLPVLAKISAYANAGVDPAIMGIGPVSATRRC 300
           SVTAGNASS+NDGAAAV++MS  KA+AL LPVLA+I A+A+ GVDPA+MGI PV ATRRC
Sbjct: 240 SVTAGNASSINDGAAAVMMMSEAKARALNLPVLARIRAFASVGVDPALMGIAPVYATRRC 299

Query: 301 LDKAGWSLEQLDLIEANEAFAAQSLAVARELKWDMDKVNVNGGAIALGHPIGASGCRVLV 360
           L++ GW L ++DLIEANEAFAAQ+L+V + L+WD  +VNVNGGAIALGHPIGASGCR+LV
Sbjct: 300 LERVGWQLAEVDLIEANEAFAAQALSVGKMLEWDERRVNVNGGAIALGHPIGASGCRILV 359

Query: 361 SLLHEMIKRDAKKGLATLCIGGGQGVALALER 392
           SL+HEM+KR+A+KGLATLCIGGGQGVAL +ER
Sbjct: 360 SLVHEMVKRNARKGLATLCIGGGQGVALTIER 391


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: 515
Number of extensions: 14
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: 393
Length adjustment: 31
Effective length of query: 362
Effective length of database: 362
Effective search space:   131044
Effective search space used:   131044
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