GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aacS in Kocuria flava HO-9041

Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate WP_058857525.1 AS188_RS02550 long-chain fatty acid--CoA ligase

Query= reanno::acidovorax_3H11:Ac3H11_3009
         (578 letters)



>NCBI__GCF_001482365.1:WP_058857525.1
          Length = 509

 Score =  247 bits (630), Expect = 9e-70
 Identities = 188/551 (34%), Positives = 272/551 (49%), Gaps = 56/551 (10%)

Query: 29  QTIGAFFADMVARQPEREALVSVHQGRRYTYAQLQTEAHRLASALLGMGLTPGDRVGIWS 88
           Q IG++    +A+  +R A+V  H GR  TYAQL    HRLA AL   G+   DRV    
Sbjct: 4   QGIGSWLDRRLAKSADRTAVV--HGGRTLTYAQLHERFHRLAGALAEAGVGRRDRVASLG 61

Query: 89  HNNAEWVLMQLATAQVGLVLVNINPAYRTAEVEYALNKVGCKLLVSMARFKTSDYLGMLR 148
            N+  ++    A   +G VLV IN    + EV Y L   G  +LV  A        G+  
Sbjct: 62  ENSPAFLEALFAAGLLGAVLVPINTRLASPEVCYQLEDAGVSVLVHDA--------GLTG 113

Query: 149 ELAPEWQGQQPGHLQAAKLPQLKTVVWIDDEAGQGADEPGLLRFTELIARGNAADPRLAQ 208
              P           A  LP +   V + +E  QG   P L    + +  G  A P    
Sbjct: 114 LAVPA----------ARDLPGITRWV-VAEEPVQGT--PTL----DAVVAG--ARPWTED 154

Query: 209 VAAGLQATDPINIQFTSGTTGFPKGATLTHRNILNNGFFIGECMKL-----TPADRLCIP 263
           V  GL+  D   I +TSGTTG PKGA LTH N      F   C+ +       AD + + 
Sbjct: 155 VPVGLE--DLAVILYTSGTTGRPKGACLTHGN------FTWNCVNVLVDYDVSADEVALM 206

Query: 264 V-PLYHCFGMVLGNLACFTHGATIVYPNDGFDPLTVLQTVQDERCTGLHGVPTMFIAELD 322
           + P++H   + +G L     GAT+V  +  F+P  VL+ ++  R T L GVPT +    +
Sbjct: 207 ISPMFHVASLGMGVLPILLKGATLVLESR-FEPGRVLELIERHRVTWLSGVPTTYQMLCE 265

Query: 323 HPRFAEFNLSTLRTGIMAGSPCPTEVMKRVVEQMNLREITIAYGMTETSPVSCQSSTDTP 382
           HP +A  +LS+LR     GS  P  V+    E   L   T +YGMTETSP     +T+ P
Sbjct: 266 HPDWARTDLSSLRKLTCGGSAVPMRVLD-AYEDRGLA-FTASYGMTETSP----GATNLP 319

Query: 383 LSKRVSTVGQVQ-PHL--EVKIVDPDTGAVVPIGQRGEFCTKGYSVMHGYWGDEAKTREA 439
            ++     G    PH   +V++V PD     P G+ GE    G +V+  YW         
Sbjct: 320 AARSREKAGSSGLPHFFSDVRVVGPDGSPAAP-GETGEILLSGPNVITEYWNRPDAAGSF 378

Query: 440 IDEGGWMHTGDLATMDAEGYVNIVGRIKDMVIRGGENIYPREIEEFLYRHPQVQDVQVVG 499
             E GW H+GDL  +DA+G++ +  R+KDM+I GGEN+YP E+E  +   P V  V V+G
Sbjct: 379 --EDGWFHSGDLGHLDADGFLFVSDRMKDMIISGGENVYPAEVEAAILELPAVAAVAVIG 436

Query: 500 VPDQKYGEELCAWIIAKPGTQPTEDDIRAFCKGQIAHYKVPRYIRFVTSFPMTVTGKIQK 559
           VPD+K+GE   A ++ + G   T + ++    G++A YKVP+ +  V   P T +GKI+K
Sbjct: 437 VPDEKWGEVPHAVVVPREGHDLTAEALQERLAGRLARYKVPKTLTLVDEMPRTASGKIRK 496

Query: 560 FKIRDEMKDQL 570
             +R E++ ++
Sbjct: 497 NVLRSELRPEV 507


Lambda     K      H
   0.320    0.136    0.412 

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: 657
Number of extensions: 34
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 578
Length of database: 509
Length adjustment: 35
Effective length of query: 543
Effective length of database: 474
Effective search space:   257382
Effective search space used:   257382
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 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