GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaK in Paraburkholderia bryophila 376MFSha3.1

Align medium-chain acyl-CoA ligase (EC 6.2.1.2); phenylacetate-CoA ligase (EC 6.2.1.30) (characterized)
to candidate H281DRAFT_05129 H281DRAFT_05129 long-chain acyl-CoA synthetase

Query= BRENDA::O74725
         (578 letters)



>FitnessBrowser__Burk376:H281DRAFT_05129
          Length = 610

 Score =  171 bits (432), Expect = 1e-46
 Identities = 155/548 (28%), Positives = 242/548 (44%), Gaps = 45/548 (8%)

Query: 50  SYSSKEVANRVDSLARSLSKEFGWAPNEGSEWDKTLAVFALNTIDSLPLFWAVHRLGGVL 109
           +Y S   +     L R  +    +  + G +    +A+   NT       + V + G V+
Sbjct: 85  AYVSVGASMTYGELGRKATAFAAYLQSIGVKPGARVAIMLPNTFQYPVSLFGVLKAGAVV 144

Query: 110 TPANASYSAAELTHQLLDSKAKALVTCVPLLSISLEAAAKAGLPKNRIYLLDVPEQLLGG 169
              N  Y+  EL HQL DS A+ ++          +A    G     + +  + + L  G
Sbjct: 145 VNVNPLYTVRELAHQLKDSGAQTIIVFENFAKTVQDALP--GSKVQNVIVTGLGDLLADG 202

Query: 170 VKPPAGY-----KSVSELTQAGKSLPPVDELRWSAGEGARRT-----------AFVCYSS 213
           +           + V ++  A  SLP    L  +   G  R            AF+ Y+ 
Sbjct: 203 LNLKGRVLNFMLRHVKKMVPA-YSLPNAVPLLKALAIGYTRPLTPVRPTHHDIAFLQYTG 261

Query: 214 GTSGLPKGVMISHRNVIANTLQIKAFEQNYRDGGGTKPASTEVALGLLPQSHIYALVVIG 273
           GT+G+ KG M++HRN+IAN LQ KA+ +    G        E  L  LP  HIY+L V  
Sbjct: 262 GTTGVAKGAMLTHRNIIANLLQAKAWAEGQLSG------EVETVLTPLPLYHIYSLTVNA 315

Query: 274 HAGAYRGDQTIVLPK-FELKSYLNAIQQYKISALFLVPPIIIHMLGTQDVCSKYDLSSVT 332
                 G + I++    ++K  +  I+  K + +  V  +    L  ++ C K D S + 
Sbjct: 316 LIFMGLGGRNILIANPRDMKRVMMIIRHEKFTGMTAVNTLYNAFLENEEFC-KRDFSDLK 374

Query: 333 SLFTGAAPLGMETAADFLKLYPNILIRQGYGLTETCTVVSSTHPHDI-----WLGSSGAL 387
               G        A  F  +    +I +GYGLTE C+ + S +P DI     + GS G  
Sbjct: 375 LAMAGGMATQRSVAERFKAVTGKPII-EGYGLTE-CSPIVSMNPVDISNLRDFEGSIGLP 432

Query: 388 LPGVEARIVTPENKEITTYDSPGELVVRSPSVVLGYLNNEKATAETFVD-GWMRTGDEAV 446
            P  + R    ++         GEL V+ P V+ GY N  + TA+   D GW+ TGD  V
Sbjct: 433 APSTQVRF-RKDDGSWANIGEAGELCVKGPQVMKGYWNRPEETAKVIDDEGWLATGDIGV 491

Query: 447 IRRSPKGIEHVFIVDRIKELIKVKGLQVAPAELEAHILAHPDVSDCAVIAIPDDRAGEVP 506
           +    +G   + ++DR K++I V G  V P E+E  I AHPDV + A I +PDD  GE  
Sbjct: 492 M--DSRGF--IRLIDRKKDMILVSGFNVYPNEIEDVIAAHPDVREVAAIGVPDDAQGERV 547

Query: 507 KAIVVKSASAGSDESVSQALVKYVEDHKARHKWLKGGIRFVDAIPKSPSGKILRRLIRDQ 566
           K  +VK   + + E V     K +  +K     +   + F D +P++  GKILRR +RD+
Sbjct: 548 KVFIVKRNPSLTAEQVIAHCRKNLTGYK-----VPKVVEFRDELPQTNVGKILRRALRDE 602

Query: 567 EKEARRKA 574
           E   ++ A
Sbjct: 603 ELAKQKTA 610


Lambda     K      H
   0.316    0.134    0.392 

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: 753
Number of extensions: 36
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 578
Length of database: 610
Length adjustment: 37
Effective length of query: 541
Effective length of database: 573
Effective search space:   309993
Effective search space used:   309993
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: 53 (25.0 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