GapMind for catabolism of small carbon sources

 

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

Align 3-hydroxybenzoate--CoA/4-hydroxybenzoate--CoA ligase; 3-hydroxybenzoyl-CoA synthetase; EC 6.2.1.27; EC 6.2.1.37 (characterized)
to candidate WP_011383961.1 AMB_RS07835 acyl-CoA synthetase AMP-fatty acid ligase

Query= SwissProt::Q9AJS8
         (523 letters)



>NCBI__GCF_000009985.1:WP_011383961.1
          Length = 500

 Score =  478 bits (1231), Expect = e-139
 Identities = 236/507 (46%), Positives = 333/507 (65%), Gaps = 10/507 (1%)

Query: 11  MNAADEIIGRPLAQGLGEQTAMLCAERSITYRELDAATNRHGNALRAHGVGKGDRVLFLM 70
           MNAADEI+G  L  G GE  A++C E+++TY +L+    R GNA+ A GV +   VL L+
Sbjct: 1   MNAADEILGPSLGSGRGESLAIICGEQTLTYDQLNRLACRFGNAMLAAGVQRQQPVLLLL 60

Query: 71  DDSPELVAAYLGTLRIGAVAVALNVRLAPRDVLYVIQDSACRLLYIDAEFLHLYQQIAGE 130
           DD PELVAAYLG ++ G VAVALN RL+P+D+ + + DS   LL  +     L  +    
Sbjct: 61  DDGPELVAAYLGAMKAGLVAVALNTRLSPKDLSHALGDSGAPLLLAETALKDLAAESLA- 119

Query: 131 LEQPPQVVVRGDEAPAPAIIAFKHFLDGQAATLESVQVAPDDVAYWLYSSGTTGRPKAVM 190
           L      +V  DE  A        FL+G +  L S  + P+D+A W+Y+SGTTG+PK  +
Sbjct: 120 LAHASARMVTTDELDA--------FLEGASDQLVSADMGPEDMALWMYTSGTTGQPKGAV 171

Query: 191 HAHRSVLIADRLEREYFGIKPGDRVFTTSKMFFGWSLGHSLMGGLQCGATVIVAPGWPDA 250
           H H S+ + +R  RE  G+ PGDR+F+TSK+FF + LGH L+G L+CG T+++  GWPDA
Sbjct: 172 HVHGSIPLGERHVRENLGLLPGDRIFSTSKLFFAYPLGHCLIGALRCGGTLVLHRGWPDA 231

Query: 251 ERVMATAARHRPTILFSTPVMYRNLLREGAGESAAMRDIRHFVSAGEKLPENIGQQWLDT 310
                  AR RP ++ S P +YR +L++G G S A R++R +VSAGE LP ++ ++W++ 
Sbjct: 232 TAAAEVIARTRPKLVLSVPSLYRIMLKDGVGSSPAFREVRTWVSAGENLPADLCRRWMEE 291

Query: 311 FGIPITEGIGASETVFLFLCARPDAYRIGSCGKRVPWAEVRLLDELGNEITTPDTPGLIA 370
            G  + EGIGA+E +FLF+ + P A + G+CG+ +PWAE +L    G  I  PDTPG + 
Sbjct: 292 TGGLMLEGIGATEALFLFIASTPTAMKPGACGRPLPWAEAQLRSPSGEVIAAPDTPGDLW 351

Query: 371 IRMASQFVGYWKLPETTEKALRDGWYYPGDMFSFDADGFWYHNGRADDMLKISGQWVSPG 430
           +RM S F  Y   P+ T++ L+DGW+  GD+FSFDA+G+W   GR+DDM+K+SGQWVSP 
Sbjct: 352 VRMDSLFRRYHNRPDVTQRVLKDGWWKTGDVFSFDAEGWWSPQGRSDDMIKVSGQWVSPS 411

Query: 431 EIESCASAVPGIAEAVVVAVPNDDGLTRLTLFIVPEDPSASQQKLSEAWMTTLRGTLSIY 490
           E+E  A  VPG+A+AV V +PN+DGL RL L+ V E     +  L    + TLR  L+IY
Sbjct: 412 EVEEAALMVPGVADAVAVGIPNEDGLVRLVLYAVAE-AGEHEPLLETRIVETLRSKLAIY 470

Query: 491 KCPRTIQFLEELPRTATGKVQKYRLRD 517
           KCPR ++FLE +PRTATGKVQ+++LR+
Sbjct: 471 KCPRNVRFLETIPRTATGKVQRFKLRE 497


Lambda     K      H
   0.321    0.137    0.417 

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: 795
Number of extensions: 30
Number of successful extensions: 3
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: 523
Length of database: 500
Length adjustment: 35
Effective length of query: 488
Effective length of database: 465
Effective search space:   226920
Effective search space used:   226920
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 (21.8 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:

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