GapMind for catabolism of small carbon sources

 

Alignments for a candidate for atoB in Marinobacter adhaerens HP15

Align acetyl-CoA C-acetyltransferase [EC: 2.3.1.9] (characterized)
to candidate GFF5 HP15_5 acetyl-CoA acetyltransferase

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



>FitnessBrowser__Marino:GFF5
          Length = 416

 Score =  543 bits (1398), Expect = e-159
 Identities = 272/392 (69%), Positives = 327/392 (83%)

Query: 1   MQEVVIVAATRTAIGSFQGSLAAIPAPELGAAVIRRLLEQTGLSGEQVDEVILGQVLTAG 60
           MQ VVIVAATRTAIGSFQG+L+   A +LGA VIR LL  T L+ E VD V++GQVL+AG
Sbjct: 24  MQGVVIVAATRTAIGSFQGALSDTSAVDLGATVIRSLLSSTSLNPELVDNVVMGQVLSAG 83

Query: 61  SGQNPARQASILAGLPHAVPALTLNKVCGSGLKALHLGAQAIRCGDAEVIIAGGMENMSL 120
            GQNPARQ++I AGLP   PA+TLNK+CGSGL++++L AQAI+C +A+V++AGGME+MS 
Sbjct: 84  CGQNPARQSAIKAGLPFTTPAMTLNKLCGSGLESVNLAAQAIQCKEADVVVAGGMESMSQ 143

Query: 121 APYVLPAARTGLRMGHAKMIDSMITDGLWDAFNDYHMGITAENLVDKYGISREEQDAFAA 180
           +PY+L  AR+GLRMGH+++ DSM+TDGL DAFN YHMG+TAENL +KY I+RE+QDAFA 
Sbjct: 144 SPYLLGKARSGLRMGHSQIEDSMLTDGLIDAFNHYHMGVTAENLAEKYQITREQQDAFAV 203

Query: 181 ASQQKAVAAIEGGRFADEITPILIPQRKGDPVAFATDEQPRAGTTAESLGKLKPAFKKDG 240
            SQ K   A+  GRF DEITP+ IPQRKG P+ F TDEQPR   ++  L KL+PAF K G
Sbjct: 204 ISQLKGSEAVASGRFKDEITPVEIPQRKGSPLKFDTDEQPRGDVSSAGLSKLRPAFAKGG 263

Query: 241 SVTAGNASSLNDGAAAVILMSAEKAKALGLPVLAKISAYANAGVDPAIMGIGPVSATRRC 300
           SVTAGNASSLNDGAAAV+LMSAEKA  LGL VLA+I +YA+A VDP+IMGIGPV ATR+C
Sbjct: 264 SVTAGNASSLNDGAAAVLLMSAEKATELGLTVLARIKSYASAAVDPSIMGIGPVPATRKC 323

Query: 301 LDKAGWSLEQLDLIEANEAFAAQSLAVARELKWDMDKVNVNGGAIALGHPIGASGCRVLV 360
           L K  WS+  LDLIEANEAFAAQ L+V +EL W+ +KVNVNGGAIALGHPIGASGCR+LV
Sbjct: 324 LAKVNWSVGDLDLIEANEAFAAQCLSVGKELGWESEKVNVNGGAIALGHPIGASGCRILV 383

Query: 361 SLLHEMIKRDAKKGLATLCIGGGQGVALALER 392
           +LL+EM +RD+KKGLATLCIGGGQGVA+ALER
Sbjct: 384 TLLYEMTRRDSKKGLATLCIGGGQGVAMALER 415


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: 502
Number of extensions: 8
Number of successful extensions: 1
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: 416
Length adjustment: 31
Effective length of query: 362
Effective length of database: 385
Effective search space:   139370
Effective search space used:   139370
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