GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hcl in Marinobacter adhaerens HP15

Align Benzoate--CoA ligase; Benzoyl-CoA synthetase; EC 6.2.1.25 (characterized)
to candidate GFF3986 HP15_3926 acyl-CoA synthetase

Query= SwissProt::Q8GQN9
         (527 letters)



>FitnessBrowser__Marino:GFF3986
          Length = 554

 Score =  173 bits (438), Expect = 2e-47
 Identities = 140/480 (29%), Positives = 215/480 (44%), Gaps = 38/480 (7%)

Query: 71  GLQPKDRVLVCVLDGIDFPTTFLGAIKGGVVPIAINTLLTESDYEYMLTDSAARVAVVSQ 130
           G++  DRVL+ + +   +  ++   ++   V I +N +   ++ E+ + D+ A V +  Q
Sbjct: 68  GVKKGDRVLLYMQNSPQYVISYYAILRADAVVIPVNPMNRSAELEHFIADTGATVCLAGQ 127

Query: 131 ELLPLFAPMLGKVPTLEHLVVAGGAG------EDSLAALLAT--------GSEQFEAA-- 174
           EL    APM+G    L+ +VVA  +       +  L A +A         G   +E A  
Sbjct: 128 ELAGFIAPMIGD-SNLDQVVVASYSTYIDPETDLDLPAEVAAPVWSRDLPGVVTWEVAMA 186

Query: 175 --------PTRPDDHCFWLYSSGSTGAPKGTVHIHSDLIHTAELYARPILGIREGDVVFS 226
                      PDD     YSSG+TGAPKG +H H  ++ TA    R    +   D V  
Sbjct: 187 AGYAPGPHTATPDDLAVIPYSSGTTGAPKGCMHTHRSVMATA--IHRIFWNLTTPDSVQL 244

Query: 227 AAKLFF-AYGLGNGLIFPLAVGATAVLMA--ERPTPAAVFERLRRHQPDIFYGVPTLYAS 283
           A   FF   G+   +  P+A GA +V+M   +R T + + ER   ++   +  + T+   
Sbjct: 245 ATLPFFHVTGMTGSMNGPIAAGAASVIMTRWDRTTASRLIER---YKVTGWTNIVTMAVD 301

Query: 284 MLANPDCPKEGELRLRACTSAGEALPEDVGRRWQARFGVDILDGIGSTEMLHIFLSNRAG 343
            L+NPD  +     L      G  +P  V  + +   G+D ++G G +E +     N   
Sbjct: 302 FLSNPDIGQYDLSSLNMIGGGGATMPSAVAEKLKRMTGLDYIEGYGLSETMAATHINPNA 361

Query: 344 DVHYGTSGKPVPGYRLRLIDEDGAEITTAGVAGELQISGPSSAVMYWNNPEKTAATFMG- 402
                  G PV     R+ID D  E    G  GE+   GP     YWN P +T A F+  
Sbjct: 362 HPKSQCLGIPVFDVDSRIIDVDTLEEKGPGETGEIVSCGPQVTRGYWNRPSETEAAFVEI 421

Query: 403 ---EWTRSGDKYLVNDEGYYVYAGRSDDMLKVSGIYVSPIEVESALIAHEAVLEAAVVGW 459
              ++ R+GD    +++GY+    R   M+  SG  V P EVE  +  H A+ E  ++  
Sbjct: 422 DGKQFFRTGDLGYYDEDGYFFMVDRVKRMINASGYKVWPSEVEGMMYRHPAIHEVCIISA 481

Query: 460 EDEDHLIKPKAFIVLKPGYGAGEALRTDLKAHVKNLLAPYKYPRWIEFVDDLPKTATGKI 519
            D       KA IVL P    G+    D+ A  K  +A YK P  I+FVD LPK+ TGK+
Sbjct: 482 PDPKRGETVKACIVLTP-EAEGQTSAGDIIAWCKEQMATYKVPTMIDFVDQLPKSPTGKL 540


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: 736
Number of extensions: 34
Number of successful extensions: 7
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: 527
Length of database: 554
Length adjustment: 35
Effective length of query: 492
Effective length of database: 519
Effective search space:   255348
Effective search space used:   255348
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: 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