GapMind for catabolism of small carbon sources

 

Alignments for a candidate for atoB in Pseudomonas fluorescens FW300-N2E3

Align acetyl-CoA C-acetyltransferase [EC: 2.3.1.9] (characterized)
to candidate AO353_01065 AO353_01065 acetyl-CoA acetyltransferase

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



>FitnessBrowser__pseudo3_N2E3:AO353_01065
          Length = 392

 Score =  627 bits (1616), Expect = 0.0
 Identities = 315/392 (80%), Positives = 348/392 (88%)

Query: 1   MQEVVIVAATRTAIGSFQGSLAAIPAPELGAAVIRRLLEQTGLSGEQVDEVILGQVLTAG 60
           M EVVIVAATRTAIGSFQG+L+AIPA ELGAAVIRRLLEQTG+   Q+DEVILGQVLTAG
Sbjct: 1   MNEVVIVAATRTAIGSFQGALSAIPATELGAAVIRRLLEQTGIDAAQIDEVILGQVLTAG 60

Query: 61  SGQNPARQASILAGLPHAVPALTLNKVCGSGLKALHLGAQAIRCGDAEVIIAGGMENMSL 120
           +GQNPARQ +I AGLPH  PALTLNKVCGSGLKA+HL  QAIRCGDAE++IAGG ENMSL
Sbjct: 61  AGQNPARQTAIKAGLPHTTPALTLNKVCGSGLKAVHLAVQAIRCGDAELVIAGGQENMSL 120

Query: 121 APYVLPAARTGLRMGHAKMIDSMITDGLWDAFNDYHMGITAENLVDKYGISREEQDAFAA 180
           APYVLP ARTGLRMGHA++ DSMI DGLWDAFNDYHMGITAENL  KY ISRE QD FAA
Sbjct: 121 APYVLPKARTGLRMGHAQLQDSMIQDGLWDAFNDYHMGITAENLAQKYEISREAQDTFAA 180

Query: 181 ASQQKAVAAIEGGRFADEITPILIPQRKGDPVAFATDEQPRAGTTAESLGKLKPAFKKDG 240
           ASQQKA AAIEGGRF  EITPILIPQRKG+P+ F TDEQPR  +TA++L KLKPAF+KDG
Sbjct: 181 ASQQKAAAAIEGGRFQSEITPILIPQRKGEPLVFDTDEQPRIDSTAQALAKLKPAFQKDG 240

Query: 241 SVTAGNASSLNDGAAAVILMSAEKAKALGLPVLAKISAYANAGVDPAIMGIGPVSATRRC 300
           SVTAGNAS+LNDGAA ++L SA KA+ALGLPVLA+I AYA+AGVDP+IMGIGPV ATR  
Sbjct: 241 SVTAGNASTLNDGAAVLLLASAAKAQALGLPVLARIKAYASAGVDPSIMGIGPVPATRLT 300

Query: 301 LDKAGWSLEQLDLIEANEAFAAQSLAVARELKWDMDKVNVNGGAIALGHPIGASGCRVLV 360
           L KAGW++E LDLIEANEAFAAQ+LAV +EL WD  KVNVNGGAIALGHPIGASG R+LV
Sbjct: 301 LQKAGWNVEDLDLIEANEAFAAQALAVGKELGWDTSKVNVNGGAIALGHPIGASGARILV 360

Query: 361 SLLHEMIKRDAKKGLATLCIGGGQGVALALER 392
           SL+HE+I+RD KKGLATLCIGGGQGV LA+ER
Sbjct: 361 SLVHELIRRDGKKGLATLCIGGGQGVGLAIER 392


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: 547
Number of extensions: 13
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: 392
Length adjustment: 31
Effective length of query: 362
Effective length of database: 361
Effective search space:   130682
Effective search space used:   130682
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