GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pimB in Pseudomonas fluorescens FW300-N2C3

Align 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized)
to candidate AO356_21640 AO356_21640 acetyl-CoA acetyltransferase

Query= metacyc::MONOMER-20679
         (395 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_21640
          Length = 393

 Score =  239 bits (610), Expect = 1e-67
 Identities = 152/401 (37%), Positives = 224/401 (55%), Gaps = 27/401 (6%)

Query: 1   MTEAVIVSTARTPIGKAYRGALNATEGATLLGHAIEHAVKRAGIDPKEVEDVVMGAAMQQ 60
           M E VIV+  RT IG +++G+L A     L    I   +++ G+  ++V++V++G  +  
Sbjct: 1   MQEVVIVAATRTAIG-SFQGSLAAIPAPELGAAVIRRLLEQTGLSGEQVDEVILGQVLTA 59

Query: 61  GATGGNIARKALLRAGLPVTTAGTTIDRQCASGLQAIALAARSVLFDGVEIAVGGGGESI 120
           G+ G N AR+A + AGLP      T+++ C SGL+A+ L A+++     E+ + GG E++
Sbjct: 60  GS-GQNPARQASILAGLPHAVPALTLNKVCGSGLKALHLGAQAIRCGDAEVIIAGGMENM 118

Query: 121 SLVQ-------------NDKMNTFHAVDPALEAIKGDVYMAMLDTAETVAKRYGISRERQ 167
           SL               + KM      D   +A   D +M +  TAE +  +YGISRE Q
Sbjct: 119 SLAPYVLPAARTGLRMGHAKMIDSMITDGLWDAFN-DYHMGI--TAENLVDKYGISREEQ 175

Query: 168 DEYSLESQRRTAAAQQGGKFNDEIAPISTKMGVVDKATGAVSFKDITLSQDEGPRPETTA 227
           D ++  SQ++  AA +GG+F DEI PI     ++ +  G      +  + DE PR  TTA
Sbjct: 176 DAFAAASQQKAVAAIEGGRFADEITPI-----LIPQRKG----DPVAFATDEQPRAGTTA 226

Query: 228 EGLAGLKAVRGEGFTITAGNASQLSDGASATVIMSDKTAAAKGLKPLGIFRGMVSYGCEP 287
           E L  LK    +  ++TAGNAS L+DGA+A ++MS + A A GL  L       + G +P
Sbjct: 227 ESLGKLKPAFKKDGSVTAGNASSLNDGAAAVILMSAEKAKALGLPVLAKISAYANAGVDP 286

Query: 288 DEMGIGPVFAVPRLLKRHGLSVDDIGLWELNEAFAVQVLYCRDKLGIDPEKLNVNGGAIS 347
             MGIGPV A  R L + G S++ + L E NEAFA Q L    +L  D +K+NVNGGAI+
Sbjct: 287 AIMGIGPVSATRRCLDKAGWSLEQLDLIEANEAFAAQSLAVARELKWDMDKVNVNGGAIA 346

Query: 348 VGHPYGMSGARLAGHALIEGRRRKAKYAVVTMCVGGGMGSA 388
           +GHP G SG R+    L E  +R AK  + T+C+GGG G A
Sbjct: 347 LGHPIGASGCRVLVSLLHEMIKRDAKKGLATLCIGGGQGVA 387


Lambda     K      H
   0.316    0.134    0.378 

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: 419
Number of extensions: 17
Number of successful extensions: 3
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: 395
Length of database: 393
Length adjustment: 31
Effective length of query: 364
Effective length of database: 362
Effective search space:   131768
Effective search space used:   131768
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