GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaK in Magnetospirillum magneticum AMB-1

Align Phenylacetate-coenzyme A ligase; Phenylacetyl-CoA ligase; PA-CoA ligase; EC 6.2.1.30 (characterized)
to candidate WP_043745126.1 AMB_RS18190 phenylacetate--CoA ligase family protein

Query= SwissProt::Q72K16
         (445 letters)



>NCBI__GCF_000009985.1:WP_043745126.1
          Length = 407

 Score =  172 bits (435), Expect = 2e-47
 Identities = 125/380 (32%), Positives = 195/380 (51%), Gaps = 23/380 (6%)

Query: 3   YQPELETLPREKLRALQEERLKRLVAYVYERVPFYRRLLDEAGVDPKGFRGLEDLPRIPF 62
           +   LET   ++  A Q E L   +A      P + R+L E  VDP    G   L R+P 
Sbjct: 4   FYDSLETRSTDEREAAQFEALPEQIALAKADSPAFARVLAE--VDPASVTGRAALARLPV 61

Query: 63  TKKTDLRDHY----PFG-LFAVPREEVARVHASSGTTGKPTVVGYTKNDLKVFAEVVARS 117
           T+K++L D      PF  L A P+ E+ RV AS G    P   G+  +  ++     AR+
Sbjct: 62  TRKSELIDAQQADPPFASLIATPKSELRRVFASPGPIYDPE--GWDNDWWRI-----ARA 114

Query: 118 LAAAGARPGMMLHNAYGYGLFTGGLGLHGGAEALGMTVVPVSGGMTERQVMLIQDFRPEV 177
           L AAG R G ++HN + Y    GG+    GA ALG  V P   G T++Q   + D +P  
Sbjct: 115 LYAAGFRRGDLMHNCFSYHFTPGGVMFETGAHALGCPVFPAGIGNTDQQAKAVADLKPAG 174

Query: 178 ISCTPSYAQTLAEEFRKRGVSPEELSLEYAVLGAEPWTEAIRKQVDEGLGVKSTNIYGLS 237
              TPS+ + + E   + G+  +  SL  A +  E     +R+ + + LGV  T  Y  +
Sbjct: 175 YGGTPSFLKIILERAEEMGL--DHSSLTKACVSGEALLPPLRQSLKD-LGVDVTQCYATA 231

Query: 238 EIIGPGVSNECVEERQGSHIWEDHFLPEVVDPDTGEPLPEGKVGVLVFTTLTKEAMPLLR 297
           ++   G+     + R+G  I ++  + E+V P TG+P+PEG+VG +V T+  ++  PL+R
Sbjct: 232 DL---GLIAYETKAREGL-IVDEGVIVEIVRPGTGDPVPEGEVGEVVVTSFNQD-YPLIR 286

Query: 298 YWTGDLTFLTYEACTCGRTHVRMGPILGRTDDMLIIRGVNVYPTQVEAVLLAIPEVVPHY 357
           + TGDL+ +      CGRT++R+   +GR D    I+G+ V+P Q+  V    PEV+   
Sbjct: 287 FATGDLSAILTGRSPCGRTNMRLKGWMGRADQTTKIKGMFVHPRQIAEVAKRHPEVI-RA 345

Query: 358 QIVVRREGTLDEAELKVEVS 377
           ++VV ++G  D   L VE S
Sbjct: 346 RLVVEKDGENDRLTLNVETS 365


Lambda     K      H
   0.319    0.139    0.409 

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: 454
Number of extensions: 35
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: 445
Length of database: 407
Length adjustment: 32
Effective length of query: 413
Effective length of database: 375
Effective search space:   154875
Effective search space used:   154875
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 51 (24.3 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