GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acs in Amycolatopsis xylanica CPCC 202699

Align acetate-CoA ligase (EC 6.2.1.1) (characterized)
to candidate WP_091300298.1 BLV57_RS42120 acetoacetate--CoA ligase

Query= BRENDA::Q2XNL6
         (634 letters)



>NCBI__GCF_900107045.1:WP_091300298.1
          Length = 658

 Score =  247 bits (631), Expect = 1e-69
 Identities = 177/590 (30%), Positives = 297/590 (50%), Gaps = 23/590 (3%)

Query: 30  WEAELEKGKDHENYWAEKAERL--EWFRKWDRVLDESNRPFYRWFVNGKINMTYNAVDRW 87
           WE  +++  +   +WA  AE L   W ++   VL  +  P  +WF  G +N   +A+   
Sbjct: 45  WEFSVQRVPE---FWAAVAEFLGMRWHQQPGEVLSGA-MPQAKWFDGGTLNYAEHALTPG 100

Query: 88  LDTDKR--NQVAILYVNERGDERKLTYYELYREVSRTANALKSLGIKKGDAVALYLPMCP 145
           +    +  +++A+++  E G  R+LTY +L  +V+    AL S G+ KGD V    P CP
Sbjct: 101 VAGASKADDELAVIFHREDGLTRQLTYGKLRAQVAAFRAALVSSGVGKGDRVVALAPNCP 160

Query: 146 ELVVSMLACAKIGAVHSVIYSGLSVGALVERLNDARAKIIITADGTYRRGGVIKLKPIVD 205
           + +V+ LA A +GAV S       V A+ +R      K+++  +G    G     +  + 
Sbjct: 161 QTLVAFLATASLGAVWSSCSPDFGVRAISDRFTQIEPKVLVAVNGYVYNGRSFDTRSTIS 220

Query: 206 EAILQCPTIETTVVVKHTDIDIEMSDISGREMLFDKLIEGEGDRCDAEEMDAEDPLFILY 265
           +   Q P++E TV++ +    +    + G     D L   +G     E +D   PL++LY
Sbjct: 221 QLREQIPSLEATVLIDY----VGGGSLDGTLDFDDLLAAHDGAELAFEPVDFAHPLWVLY 276

Query: 266 TSGSTGKPKGVLHTTGGYMVGVASTLEMTFDIHNGDLWWCTADIGWITGHSYVVYGPLLL 325
           +SG+TG PKG++H  GG  + +   L +  D+  GD ++     GW+   ++++ G LL+
Sbjct: 277 SSGTTGLPKGIVHGHGGITIELLKALALQSDLGPGDRFFWFTTTGWMM-WNFLISG-LLV 334

Query: 326 GTTTLLYEGAPDYPDPGVWWSIVEKYGVTKFYTAPTAIRHLMRFGDKHPKRYNLESLKIL 385
           GTT +L++G+P +PD  V W + E++ VT F T+   I+  ++ G K   +Y+L +L+ +
Sbjct: 335 GTTIVLFDGSPGHPDLNVLWHLAEQHRVTFFGTSAPFIQSCLKEGIKPSSKYDLTALRAI 394

Query: 386 GTVGEPINPEAWMWYYRNIGREKCPIIDTWWQTETGMHLIAPLPVTPLKPGSVTKPLPGI 445
           G+ G P++ E + W     G+    I      T+     +A  P  P+  G ++    G 
Sbjct: 395 GSTGSPLSVEGFRWLVNEFGK-SVQICSVSGGTDLCAAFVAASPDLPVWLGELSCRALGA 453

Query: 446 EADVVDENGDPVPLGKGGFLVIRKPWPAMFRTLFNDE--QRYIDVYWKQIPGGVYTAGDM 503
             +  DE G+ V + + G LV+ +P P+M    +ND    R  + Y++  P G++  GD 
Sbjct: 454 AVESFDEAGNSV-IEEVGELVVTQPMPSMPVYFWNDPDGSRLREAYFEMYP-GIWRHGDW 511

Query: 504 ARKDEDGYFWIQGRSDDVLNIAGHRIGTAEVESVFVAHPAVAEAAVI--GKADPIKGEVI 561
            R  + G   I GRSD  LN  G R+GTAE   V     +VA++ VI    A    G+++
Sbjct: 512 IRITKRGSAVIYGRSDSTLNRGGVRMGTAEFYRVVEGFASVADSLVIDTSAAGNEDGQLL 571

Query: 562 KAFLILKKGHKLNAALIEELKRHLRHELGPVAVVGEMVQVDSLPKTRSGK 611
             FL+LK G  L A +   L++ LR  L P  V    V V  +P+T +GK
Sbjct: 572 -CFLVLKSGASL-ADVEPSLRKELRGALSPRHVPDRFVVVTEIPRTLNGK 619


Lambda     K      H
   0.319    0.138    0.428 

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: 1082
Number of extensions: 58
Number of successful extensions: 5
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: 634
Length of database: 658
Length adjustment: 38
Effective length of query: 596
Effective length of database: 620
Effective search space:   369520
Effective search space used:   369520
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: 54 (25.4 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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