GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hcl in Thermithiobacillus tepidarius DSM 3134

Align 4-hydroxybenzoate--CoA/benzoate--CoA ligase; 4-hydroxybenzoyl-CoA synthetase; EC 6.2.1.25; EC 6.2.1.27 (characterized)
to candidate WP_028989221.1 G579_RS0104490 acetate--CoA ligase

Query= SwissProt::Q53005
         (539 letters)



>NCBI__GCF_000423825.1:WP_028989221.1
          Length = 652

 Score =  148 bits (373), Expect = 7e-40
 Identities = 147/562 (26%), Positives = 246/562 (43%), Gaps = 62/562 (11%)

Query: 5   DYNAAVDFVDRNVAEGRGGKIAFI-----DPQRSLSYGELRDAVARVGPMLARLGVEQEN 59
           + N A + +DR+++     K A I        R+ +YG+L   V+R   +L +LG+   +
Sbjct: 81  ELNVAANCLDRHLSSPTRNKAALIWEGEDGEVRTFTYGQLHREVSRFANVLKKLGITTGD 140

Query: 60  RIALVLKDTVDFPILFWGAIRAGIVPVLLNTRLTADQYRYLLEDSRSRVVFASSEFLPVI 119
           R+A+ +    +  +      R G +  ++    +A+  +  +ED++++++  +       
Sbjct: 141 RVAIYMPMVPEAAVAMLACARLGAIHSVVFGGFSAEALKDRIEDTQAKLLITADGGF--- 197

Query: 120 EEAAADLPHLR-----TIIAVGDAPAPTLQLANL----------------LATEQEGGAP 158
              A  + HL+      ++  G +    + L                   L  + E   P
Sbjct: 198 --RAGRVVHLKQHADQALMRDGHSVDKVVVLRRTGQEVDMLDGRDLWWHELMQDAEPQCP 255

Query: 159 AATC-ADDIAYWQYSSGTTGMPKGVMHVHSSPRVMAENAGRRI-GYREDDVVFSAAKLFF 216
           A +  A+   +  Y+SG+TG PKG++H      + +    R +   + +DV +  A + +
Sbjct: 256 AVSVNAEHPLFVLYTSGSTGKPKGIVHSSGGYLLWSALTMRWVFDIKPEDVYWCTADIGW 315

Query: 217 AYGLGNAMFCPMGIGATSVLY---PERPTADSVFDTLRLHQPTLLFAVPTLYAAMLADPR 273
             G   A++ P+ +GAT +L+   P  P A   +  +  H  ++ +  PT   A++    
Sbjct: 316 VTGHTYALYGPLAVGATVLLFEGVPTYPDAGRFWAMIERHGVSVFYTAPTAVRALM---- 371

Query: 274 SRTETLPDR-----LRLCVSAGEPLPAQVGLNWRNRFGHD---IVNGVGSTEMGHLFLTN 325
              E  P +     LRL  + GEP+  +  + +    G +   +V+    TE G   +  
Sbjct: 372 KLGEEWPGKYDLSSLRLLGTVGEPINPEAWMWYYRVIGKERCPVVDTWWQTETGGHLIAP 431

Query: 326 LPHA--VEYGTSGVPVDGYRLRLVGDRGQDVADDEIGELLVSG----GSSAAGYWNQRDK 379
           LP    ++ G+   P+ G    +V + G  V   E G  LV      G     + N    
Sbjct: 432 LPGVTPLKPGSCTRPLPGIFPDIVDEEGDPVQGTEAGGYLVVKRPWPGMLRTVWGNDARY 491

Query: 380 TRT---TFVGEWTRTGDKYHRRADGVYTYCGRTDDIFKVSGIWVSPFEIEQALMSHAKVL 436
             T    F   +   GD  HR ADG Y   GR DD+  VSG  +   EIE AL+SH  V 
Sbjct: 492 LETYWAKFQNRYYVAGDSAHRDADGYYWIMGRIDDVLNVSGHRLGTMEIESALVSHPAVA 551

Query: 437 EAAVI--PAEDTDGLIKPKAFIVL-ASRGDIDPGALFDELKEHVKSAIGPWKYPRWIQIM 493
           EAAV+  P E     I   AF++L  S    D   L + L++HV  AIGP   P  I+  
Sbjct: 552 EAAVVGRPHEIKGEAI--TAFVILRQSHVQDDRDRLTEALRQHVSEAIGPIAKPDDIRFT 609

Query: 494 DDLPKTSSGKLQRYLLREMTLG 515
           D+LPKT SGK+ R LLR +  G
Sbjct: 610 DNLPKTRSGKIMRRLLRAIARG 631


Lambda     K      H
   0.320    0.138    0.415 

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: 925
Number of extensions: 40
Number of successful extensions: 5
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: 539
Length of database: 652
Length adjustment: 37
Effective length of query: 502
Effective length of database: 615
Effective search space:   308730
Effective search space used:   308730
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 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