GapMind for catabolism of small carbon sources

 

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

Align phenylacetate-CoA ligase (EC 6.2.1.30) (characterized)
to candidate WP_043745116.1 AMB_RS18140 malonyl-CoA synthase

Query= BRENDA::A7KUK6
         (562 letters)



>lcl|NCBI__GCF_000009985.1:WP_043745116.1 AMB_RS18140 malonyl-CoA
           synthase
          Length = 508

 Score =  174 bits (440), Expect = 1e-47
 Identities = 146/484 (30%), Positives = 229/484 (47%), Gaps = 35/484 (7%)

Query: 68  RKGDVLALFTPNSIDTPVVMWGTLWAGGTISPANPGYTVDELAFQLKNSHAKGLVTQASV 127
           + GD +A+    S +  V+    L +G  + P N  Y   EL + L ++    +V Q S 
Sbjct: 52  KPGDRVAVQVDKSAEAVVLYLACLRSGAVLLPLNTAYQAGELEYFLFDAAPSAVVCQPSR 111

Query: 128 LPVAREAAKKVGMPEDRIILIGDQRDPDARVKHFTSVRNISGATRYRKQKITPAKDVAFL 187
           L      A   G+    ++ +G   D        T      G +           D+A +
Sbjct: 112 LAELEGLAVAAGIGTC-VMTLGSHGDG-------TLPERAKGLSETFATVPRGGDDMAAI 163

Query: 188 VYSSGTTGVPKGVMISHRNIVANIRQQFIAEGEMLSWNGGPDGKGDRVLAFLPFYHIYGL 247
           +YSSGTTG PKG M+SH N+ +N      A+     W   PD   D +L  LP +H +GL
Sbjct: 164 LYSSGTTGRPKGAMMSHTNLGSN------AQTLHDLWGFRPD---DVLLHCLPIFHTHGL 214

Query: 248 TCLITQALYKGYHLIVMSKFDIEKWCAHVQNYRCSFSYIVPPVVLLLGKHPVVDKYDLSS 307
              I   L  G  +I   KFD E+    ++  R +    VP         P +     S 
Sbjct: 215 FVAINCVLLNGSPMIFCPKFDAEQAIGLLK--RATVFMGVPTFYTRFLTSPNLTPEACSH 272

Query: 308 LRMMNSGAAPLTQELVEAVYSRIKVGIKQGYGLSETSPTTHSQRWEDWREAMGSVGRLMP 367
           +R+  SG+APL +E   A   +    I + YG++E    T +    D R   G+VG  +P
Sbjct: 273 MRLFISGSAPLLEETFNAFKDKTGFTILERYGMTEGGMFTSNPLVGDRRA--GTVGFPLP 330

Query: 368 NMQAKYMTMPEDGSEPKEVGEGEVGELYLKGPNVFLGYHENPEATKGCLSEDGWFQTGDV 427
           ++Q +       G E + + +GEVG + +KGPN+F GY   PE TK   +EDG+F++GDV
Sbjct: 331 DVQLRIT-----GEEGQVLPQGEVGIIEVKGPNIFKGYWNMPEKTKSDFTEDGFFKSGDV 385

Query: 428 GYQDAKGNFYITDRVKELIKYKGFQVPPAELEGYLVDNDAIDDVAVIGIESETHGSEVPM 487
           G  DA+G   I  R K+LI   G+ V P E+E ++     + + AV+G+     G E  +
Sbjct: 386 GVVDARGYVSIVGRAKDLIISGGYNVYPKEVEDFIDRLAGVVESAVVGMPHPDFG-EAGL 444

Query: 488 ACVVRSAKSKSSGTSEKDEAARIIKWLDSKVASHKRLRGGVHFVDEIPKNPSGKILRRIL 547
           A VV  A+  +S T+E      +I  L  ++A++K  +  V  V E+P+N  GK+ + +L
Sbjct: 445 AIVV--AEKGASLTAE-----GVIDSLKGRLANYKVPKLAV-VVTELPRNAMGKVQKNVL 496

Query: 548 KQKF 551
           +  +
Sbjct: 497 RDSY 500


Lambda     K      H
   0.317    0.136    0.410 

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: 674
Number of extensions: 40
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: 562
Length of database: 508
Length adjustment: 35
Effective length of query: 527
Effective length of database: 473
Effective search space:   249271
Effective search space used:   249271
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 (21.7 bits)
S2: 52 (24.6 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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