GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pcaF in Echinicola vietnamensis KMM 6221, DSM 17526

Align Beta-ketoadipyl-CoA thiolase; 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized)
to candidate Echvi_3705 Echvi_3705 acetyl-CoA acetyltransferases

Query= SwissProt::Q8VPF1
         (401 letters)



>FitnessBrowser__Cola:Echvi_3705
          Length = 393

 Score =  251 bits (641), Expect = 3e-71
 Identities = 158/402 (39%), Positives = 232/402 (57%), Gaps = 14/402 (3%)

Query: 3   REVYICDAVRTPIGRFGGSLAAVRADDLAAVPVKALVERNPQVDWSQLDEVYLGCANQAG 62
           +EVYI  AVRTP+G FGG L+ + A +L A  +K  + R  QV   Q+DEV +G    A 
Sbjct: 2   KEVYIISAVRTPLGSFGGKLSGLTAVELGAQAIKGALGR-AQVTPEQVDEVIMGNVLSAN 60

Query: 63  EDNRNVARMALLLAGLPDSVPGVTLNRLCASGMDAVGTAFRAIASGEAELVIAGGVESMS 122
              +  AR A + AG+   VP  T+N++CASGM +V  A ++I +G++++++AGG+ESMS
Sbjct: 61  L-GQAPARQAAIGAGIGYHVPCTTVNKVCASGMKSVMFAAQSIMTGQSDIIVAGGMESMS 119

Query: 123 RAPYVMGKADSA--FGRGQKIEDTTIGWRFINPLMKAQYGVDAMPETADNVADDYKVSRA 180
             PY + KA     FG G+ ++         + L +  Y    M   ADN A +  +SR 
Sbjct: 120 NVPYYIPKARFGYKFGNGEFVDGLAK-----DGLHEVYYNFP-MGNCADNTAKEKNISRE 173

Query: 181 DQDAFALRSQQLAGRAQAAGYFAEEIVPVVIKGKKGETV-VDADEHLRPDTTLEALAKLK 239
            QD +A++S + A  A  A  F +E++PV  K +KGE++ VD DE  + +   E +  L+
Sbjct: 174 AQDEYAIQSYRRAAEAWKAQAFQDEVIPVTFKSRKGESITVDEDEEYQ-NVLFEKIPSLR 232

Query: 240 PVNGPDKTVTAGNASGVNDGSVALILASAEAVKKHGLKARAKVLGMASAGVAPRVMGIGP 299
           PV   + TVTA NAS +NDG+ AL+L S E  +  GL+  AK+LG A A   P      P
Sbjct: 233 PVFDKEGTVTAANASTMNDGAAALVLMSKEKAEALGLQPVAKILGFADAATDPIWFTTAP 292

Query: 300 VPAVRKLLERLNLSVADFDVIELNEAFAAQGLAVTRELGIADDDARVNPNGGAIALGHPL 359
             A+ K L+   +     D  E+NEAF+A  LA  +EL I +D  R+N  GGA++LGHPL
Sbjct: 293 ALAIPKALKNAGIQAEAVDYYEINEAFSAVALANQQELNIPND--RLNVFGGAVSLGHPL 350

Query: 360 GASGARLVLTAVHQLEKSGGQRGLCTMCVGVGQGVALAVERV 401
           GASGAR++ T    L + GG+ G+  +C G G   A+ +E +
Sbjct: 351 GASGARIMATLHSVLRQKGGKIGVAGICNGGGGASAMVIENL 392


Lambda     K      H
   0.317    0.134    0.379 

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: 401
Number of extensions: 20
Number of successful extensions: 4
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: 401
Length of database: 393
Length adjustment: 31
Effective length of query: 370
Effective length of database: 362
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