GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaJ2 in Lactobacillus delbrueckii ZN7a-9

Align Beta-ketoadipyl-CoA thiolase; 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized)
to candidate WP_002877493.1 B506_RS01555 thiolase family protein

Query= SwissProt::Q8VPF1
         (401 letters)



>NCBI__GCF_000387565.1:WP_002877493.1
          Length = 366

 Score =  250 bits (638), Expect = 5e-71
 Identities = 163/402 (40%), Positives = 223/402 (55%), Gaps = 42/402 (10%)

Query: 3   REVYICDAVRTPIGRFGGSLAAVRADDLAAVPVKALVERNPQVDWSQLDEVYLGCANQAG 62
           +++YI  A RTP GR+   LA   A DL  + ++  + +   +D   LD +++G    AG
Sbjct: 2   QDIYIVAAKRTPFGRYHKQLADFSAIDLGQIALRGAL-KEAGLDAKALDALFMGNVLSAG 60

Query: 63  EDNRNVARMALLLAGLPDSVPGVTLNRLCASGMDAVGTAFRAIASGEAELVIAGGVESMS 122
              +N+AR   L AG+      V++N +C S + A   A   +  G+  LV  GG ESM+
Sbjct: 61  L-GQNIARQIALNAGMRQDSVAVSINEVCGSSLKAARLAEAQMLIGDLGLVAVGGSESMT 119

Query: 123 RAP----YVMGKADSAFGRGQKIEDTTIGWRFINPLMKAQYGVDAMPETADNVADDYKVS 178
            AP    +  G  DS  G+   I                         TA+NVA    +S
Sbjct: 120 NAPKEIMFSDGLVDSFSGKSMGI-------------------------TAENVAKRNHIS 154

Query: 179 RADQDAFALRSQQLAGRAQAAGYFAEEIVPVVIKGKKGETVVDADEHLRPDTTLEALAKL 238
           R D DAF+L S Q A +AQA G FA+EI+ +          +  DE++RPDT+LEALA L
Sbjct: 155 RQDADAFSLSSHQKAVKAQAEGLFADEIIQI--------EDLKQDENVRPDTSLEALAGL 206

Query: 239 KPVNGPDKTVTAGNASGVNDGSVALILASAEAVKKHGLKARAKVLGMASAGVAPRVMGIG 298
           K     D TVTAGNAS ++DG+  +ILA+AE V ++ L   AK+   A  G  P  MG G
Sbjct: 207 KTSFLEDGTVTAGNASPISDGASMIILATAEKVAEYQLTPLAKLGAYAEVGYDPEFMGYG 266

Query: 299 PVPAVRKLLERLNLSVADFDVIELNEAFAAQGLAVTRELGIADDDARVNPNGGAIALGHP 358
           P  A+RKLL+     VAD+D  E+NEAFAA  LAV R+L I    A+VN  GGAIALGHP
Sbjct: 267 PYYAIRKLLDETGRQVADYDFFEINEAFAATTLAVARDLEI--PLAKVNKQGGAIALGHP 324

Query: 359 LGASGARLVLTAVHQLEKSGGQRGLCTMCVGVGQGVALAVER 400
           LGASG RL+ TA  QL++ GGQR + ++C+G G  +A  +E+
Sbjct: 325 LGASGTRLLATAARQLQR-GGQRAIASLCIGGGLAIAFEIEK 365


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: 365
Number of extensions: 19
Number of successful extensions: 6
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: 366
Length adjustment: 30
Effective length of query: 371
Effective length of database: 336
Effective search space:   124656
Effective search space used:   124656
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 24 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