GapMind for catabolism of small carbon sources

 

Alignments for a candidate for atoB in Herbaspirillum seropedicae SmR1

Align acetyl-CoA C-acetyltransferase [EC: 2.3.1.9] (characterized)
to candidate HSERO_RS20660 HSERO_RS20660 acetyl-CoA acetyltransferase

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



>FitnessBrowser__HerbieS:HSERO_RS20660
          Length = 401

 Score =  314 bits (805), Expect = 2e-90
 Identities = 179/399 (44%), Positives = 251/399 (62%), Gaps = 10/399 (2%)

Query: 3   EVVIVAATRTAIGSFQGSLAAIPAPELGAAVIRRLLEQT-GLSGEQVDEVILGQVLTAGS 61
           E +I  A RT  G + G+L A+ A +L AA IR L+E+  G+   +V++++ G    AG 
Sbjct: 2   EALICDAIRTPFGRYGGALGAVRADDLAAAPIRSLMERNPGVDWSRVEDILYGCANQAGE 61

Query: 62  -GQNPARQASILAGLPHAVPALTLNKVCGSGLKALHLGAQAIRCGDAEVIIAGGMENMSL 120
             +N AR A +LAGLP AVP  T+N++CGS L A+ + A+AI+ G+ +++IAGG+E+M+ 
Sbjct: 62  DNRNVARMAGLLAGLPIAVPGSTVNRLCGSSLDAVGMAARAIKSGEVQLMIAGGVESMTR 121

Query: 121 APYVLPAARTGLRMGHAKMIDSMITDGLWDAFNDYHMGI-----TAENLVDKYGISREEQ 175
           AP+V+  A +      A + D+ I     +       GI     TAEN+   + I+R +Q
Sbjct: 122 APFVMGKAESAFARS-AAIFDTTIGWRFVNPLMKAQYGIDSMPETAENVATDFQINRADQ 180

Query: 176 DAFAAASQQKAVAAIEGGRFADEITPILIPQRKGDPVAFATDEQPRAGTTAESLGKLKPA 235
           DAFA  SQQ+  AA   G FA EI P+ IPQ+KGDP+   TDE PR  TT  +L KLK  
Sbjct: 181 DAFALRSQQRWAAAQAAGFFAGEIAPLTIPQKKGDPLVVTTDEHPRPDTTLATLAKLKGV 240

Query: 236 FKKDGSVTAGNASSLNDGAAAVILMSAEKAKALGLPVLAKISAYANAGVDPAIMGIGPVS 295
            + DG+VTAGNAS +NDGA A++L S + A    L   A++   A AGV P IMG GP  
Sbjct: 241 VRPDGTVTAGNASGVNDGACALLLASPKAADLYRLKPRARVLGMATAGVAPRIMGFGPAP 300

Query: 296 ATRRCLDKAGWSLEQLDLIEANEAFAAQSLAVARELKW--DMDKVNVNGGAIALGHPIGA 353
           A R+ L + G +L Q+D+IE NEAFAAQ LAV R+L    D   VN NGGAIA+GHP+GA
Sbjct: 301 AVRKVLAQVGLTLAQMDVIELNEAFAAQGLAVMRDLGLPDDAAHVNPNGGAIAIGHPLGA 360

Query: 354 SGCRVLVSLLHEMIKRDAKKGLATLCIGGGQGVALALER 392
           SG R++ + ++++ +   +  L T+CIG GQG+AL +ER
Sbjct: 361 SGARLVTTAINQLERSGGRYALCTMCIGVGQGIALVIER 399


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: 381
Number of extensions: 16
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: 393
Length of database: 401
Length adjustment: 31
Effective length of query: 362
Effective length of database: 370
Effective search space:   133940
Effective search space used:   133940
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