GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hcl in Desulfurobacterium atlanticum DSM 15668

Align Benzoate--CoA ligase; Benzoyl-CoA synthetase; EC 6.2.1.25 (characterized)
to candidate WP_089322819.1 CHB58_RS03975 acetate--CoA ligase

Query= SwissProt::Q8GQN9
         (527 letters)



>NCBI__GCF_900188395.1:WP_089322819.1
          Length = 631

 Score =  155 bits (391), Expect = 5e-42
 Identities = 145/545 (26%), Positives = 236/545 (43%), Gaps = 48/545 (8%)

Query: 23  NAADDLIGRNLLAGRGGKTVYI--DDAGS---YTYDELALRVNRCGSALRTTLGLQPKDR 77
           N   + + R++  GR  K  +   D+ G+    TY  L   VN+  +AL+   G++  DR
Sbjct: 79  NITVNALDRHVKNGRKNKVAFFWEDEFGNEKVVTYGSLYTLVNKLANALKNA-GIKKGDR 137

Query: 78  VLVCVLDGIDFPTTFLGAIKGGVVPIAINTLLTESDYEYMLTDSAARVAVVSQ------- 130
           V++ +   ++     L   + G V   +    +     + + D+ A++ + +        
Sbjct: 138 VVIYMPLVVEQVAAMLACARIGAVHSVVYAGFSVPALRHRIEDAQAKMVITADMTIRRGR 197

Query: 131 --ELLPLFAPMLGKVPTLEHLVVAG---------GAGEDSLAALLATGSEQFEAAPTRPD 179
              L  +    +  +  +E +VV           G  E      +       E      +
Sbjct: 198 AIPLKQIVDEAVRGLDNVEKVVVLRRLKPKVDLIGEKEIDFYEFIKDADTYCEPEVMDSE 257

Query: 180 DHCFWLYSSGSTGAPKGTVHIHSDLIHTAELYARPILGIREGDVVFSAAKLFFAYGLGNG 239
           D  F LY+SGSTG PKG +H     +       + +  ++E D+ +  A   +  G    
Sbjct: 258 DPLFMLYTSGSTGKPKGVIHTTGGYMVGTYYSMKTVFDLKEDDIYWCTADPGWITGHSYI 317

Query: 240 LIFPLAVGATAVLMAERPTPAAV---FERLRRHQPDIFYGVPT-LYASMLANPDCPKEGE 295
           +  PL  GAT VL    P        +  + ++   IFY  PT +   M A    P++ +
Sbjct: 318 VYGPLVAGATQVLAEGAPNYPDFGRWWSLIEKYGVTIFYTAPTAIRMFMRAGEHWPEKYD 377

Query: 296 LR-LRACTSAGEALPEDVGRRWQARFGV------DILDGIGSTEMLHIFLSNRAG-DVHY 347
           L  LR   S GE +  +    W   F V       I+D    TE   + ++   G  +  
Sbjct: 378 LSSLRLLGSVGEPINPEA---WMWYFRVIGKERCPIVDTWWQTETGAVMITTIDGLPMKP 434

Query: 348 GTSGKPVPGYRLRLIDEDGAEITTAGVAGELQISGPSSAVMYWNNPEKTAATFMGEWTR- 406
           G +GKPVPG    ++D++G  +      G L +  P  ++M      K    +   W   
Sbjct: 435 GRAGKPVPGVVADVVDKEGNPVEP-NKGGFLVVRNPWPSMM--RTIHKNKEKYESYWNTI 491

Query: 407 -----SGDKYLVNDEGYYVYAGRSDDMLKVSGIYVSPIEVESALIAHEAVLEAAVVGWED 461
                +GD    +++GY +  GR+DD++ VSG  +  +EVESAL++H +V EAAV+G  D
Sbjct: 492 PGCYFAGDVATKDEDGYIMILGRADDVINVSGHRIGTMEVESALVSHPSVAEAAVIGKPD 551

Query: 462 EDHLIKPKAFIVLKPGYGAGEALRTDLKAHVKNLLAPYKYPRWIEFVDDLPKTATGKIQR 521
                + KAF++LK G    E L   LK HV+  L     P  IEFVD LPKT +GKI R
Sbjct: 552 PVKGERIKAFVILKEGESPSEELVNSLKKHVRTELGALAVPSEIEFVDKLPKTRSGKIMR 611

Query: 522 FKLRS 526
             L++
Sbjct: 612 RVLKA 616


Lambda     K      H
   0.319    0.138    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: 879
Number of extensions: 61
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: 527
Length of database: 631
Length adjustment: 36
Effective length of query: 491
Effective length of database: 595
Effective search space:   292145
Effective search space used:   292145
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: 53 (25.0 bits)

This GapMind analysis is from Apr 09 2024. 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