GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aacS in Amantichitinum ursilacus IGB-41

Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate WP_053937789.1 WG78_RS10575 long-chain-fatty-acid--CoA ligase FadD

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



>NCBI__GCF_001294205.1:WP_053937789.1
          Length = 554

 Score =  221 bits (562), Expect = 8e-62
 Identities = 168/536 (31%), Positives = 260/536 (48%), Gaps = 26/536 (4%)

Query: 39  VARQPEREALVSVHQGRRYTYAQLQTEAHRLASALLG-MGLTPGDRVGIWSHNNAEWVLM 97
           VAR  +R+A +++  G+  TY +L   +   A+ L   + L+ G RVGI   N  ++ + 
Sbjct: 33  VARYADRDAFINM--GKAITYQELDQLSTAFAAYLQQTLRLSRGARVGIMMPNLLQYPVA 90

Query: 98  QLATAQVGLVLVNINPAYRTAEVEYALNKVGCKLLVSMARFK-TSDYLGMLRELAPEWQG 156
                + G+V+VNINP Y   E+E+ L   G + +V +A F  T D       +      
Sbjct: 91  LFGILKAGMVVVNINPLYTPRELEHQLKDSGAEAIVIVANFAHTLDKCIGKTAVKHVIVS 150

Query: 157 QQPGHLQAAKLPQLKTVVWIDDEAGQGADEPGLLRFTELIARGNAADPRLAQVAAGLQAT 216
           Q    L   K   +  V+    +     + PG + F   +A G A    LA V   L   
Sbjct: 151 QIGDMLDFPKRQLVNAVIKYIKKMVPAYNLPGAVSFNHALADGRAQT--LAPV--NLTLD 206

Query: 217 DPINIQFTSGTTGFPKGATLTHRNILNN--------GFFIGECMKLTPADRLCIPVPLYH 268
           D   +Q+T GTTG  KGA LTHRNI+ N        G  + +  +L     +   +PLYH
Sbjct: 207 DLAFLQYTGGTTGVAKGAMLTHRNIVANMQQAHAWIGGVVADGREL-----IVTALPLYH 261

Query: 269 CFGMVLGNLACFTHGATIVYPNDGFDPLTVLQTVQDERCTGLHGVPTMFIAELDHPRFAE 328
            F +    +     GAT +   +  D    ++ +     T + GV T+F A ++HP F +
Sbjct: 262 IFSLTANGMIFTKIGATNLLITNPRDIPGFIKELGKYPVTAITGVNTLFNALVNHPDFLK 321

Query: 329 FNLSTLRTGIMAGSPCPTEVMKRVVEQMNLREITIAYGMTETSPVSCQSSTDTPLSKRVS 388
            + S+ +  +  G      V  +  +   +  +  AYG+TETSP +  +     L +   
Sbjct: 322 LDFSSWKLTLGGGMAVQQPVADKWKKVTGVTLVE-AYGLTETSPAAMINPMT--LREYNG 378

Query: 389 TVGQVQPHLEVKIVDPDTGAVVPIGQRGEFCTKGYSVMHGYWGDEAKTREAIDEGGWMHT 448
            +G   P  + +I   D G+V P G  GE   KG  VM GYW    +T + I   G++ T
Sbjct: 379 MIGLPVPSTDAQIRGED-GSVQPPGSAGELFIKGPQVMKGYWQRADETAKVIGADGYLAT 437

Query: 449 GDLATMDAEGYVNIVGRIKDMVIRGGENIYPREIEEFLYRHPQVQDVQVVGVPDQKYGEE 508
           GD+A M   G+  I  R KDMV+  G N+YP E+E+ + RHP V +V  VGVPD K GE 
Sbjct: 438 GDVAIMSPTGFFRIADRKKDMVLVSGFNVYPNEVEDVVARHPGVLEVACVGVPDDKSGEA 497

Query: 509 LCAWIIAKPGTQPTEDDIRAFCKGQIAHYKVPRYIRFVTSFPMTVTGKIQKFKIRD 564
           +  +++ K  T  TE  + A+C+ Q+ +YKVPR + F  + P +  GKI + ++RD
Sbjct: 498 VKIFVVRKDPTL-TEAALIAYCREQLTNYKVPRKVEFRDALPKSNVGKILRRELRD 552


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: 739
Number of extensions: 48
Number of successful extensions: 7
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: 578
Length of database: 554
Length adjustment: 36
Effective length of query: 542
Effective length of database: 518
Effective search space:   280756
Effective search space used:   280756
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: 53 (25.0 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