GapMind for catabolism of small carbon sources

 

Alignments for a candidate for prpE in Thermoactinomyces daqus H-18

Align propionate-CoA ligase (EC 6.2.1.17); 3-hydroxypropionyl-CoA synthase (EC 6.2.1.36) (characterized)
to candidate WP_033100144.1 JG50_RS0105805 AMP-binding protein

Query= BRENDA::A4YGR1
         (661 letters)



>NCBI__GCF_000763315.1:WP_033100144.1
          Length = 646

 Score =  430 bits (1105), Expect = e-124
 Identities = 247/628 (39%), Positives = 373/628 (59%), Gaps = 20/628 (3%)

Query: 29  RYYAHLMKLSKEKPAEFWGSLAQDL-LDWYEPWKETMRQEDPM--TRWFIGGKINASYNA 85
           R Y    + S +  A FW  +  DL L W  P+++ +   D +  TRWF+ GKIN S N 
Sbjct: 28  RDYDRFYEQSIKNIAWFWDEVVNDLGLRWMMPYRQVLDMSDGIAWTRWFVDGKINISDNC 87

Query: 86  VDRHLNGPR-KFKAAVIWESELGERKIVTYQDMFYEVNRWANALRSLGVGKGDRVTIYMP 144
           +DR +  P  + + A+IWE + G  K  TY+D++ EVNR A  L+ LGV  GD V IYMP
Sbjct: 88  LDRFVEEPAARHRLALIWEGDDGTTKKYTYRDLWLEVNRLACGLKKLGVAAGDCVAIYMP 147

Query: 145 LTPEGIAAMLASARIGAIHSVIFAGFGSQAIADRVEDAKAKVVITADAYPRRGKVVELKK 204
           +  E + AMLA ARIGAI +  F+G+G++A+A R++  +AK +ITAD Y RRGKVV +K+
Sbjct: 148 MIAENVIAMLAVARIGAIFTPCFSGYGAEAVATRIQGCQAKWLITADGYLRRGKVVAMKE 207

Query: 205 TVDEALNSLGERSP-VQHVLVYRRMKTDVNMKEGRDVFFDEV-GKYRYVEPERMDSNDPL 262
             D A     + SP V+ V+V  R+  D      RDV +D++  + + + P   D+NDP 
Sbjct: 208 EADRA----ADLSPSVEKVVVVSRLGRDCPWNPDRDVKWDQLTAEMKTLSPAVTDANDPF 263

Query: 263 FILYTSGTTGKPKGIMHSTGGYLTGTAVMLLWSYGLSQENDVLFNTSDIGWIVGHSYITY 322
            I+YTSGTTGKPKG +H   G+    A    +++ +    D+LF  +D+GW++G  ++ +
Sbjct: 264 MIIYTSGTTGKPKGTVHVHSGFPLKAAFDAGYAFDVG-PGDILFWVTDMGWMMG-PWMVF 321

Query: 323 SPLIMGRTVVIYESAPDYPYPDKWAEIIERYRATTFGTSATALRYFMKYGDEYVKNHDLS 382
             L++G T++++E  PDYP P +  E+ E++  T  G S T +R  MK+G  +    DLS
Sbjct: 322 GTLLLGSTMLVFEGTPDYPIPGRLWELTEKHGVTHLGISPTLIRALMKHGTSWFSQRDLS 381

Query: 383 SIRIIVTNGEVLNYSPWKWGLEVLGGGKVFMSHQWWQTETGAPNLGYLPGIIYMPMKSGP 442
           S+R+  + GE  N  PW W  E +GG +V + +    TE      G L    + P+    
Sbjct: 382 SLRVFGSTGEPWNPEPWHWLFEQVGGKRVPIFNYSGGTEISG---GILGNHFFKPIVPCG 438

Query: 443 ASGFPLPGNFVEVLDENGNPSAPRVRGYLVMRPPFPPNMMMGMWNDNGERLKKTYFSKFG 502
            +G PLPG   EV D+ G      V G LV+R P+   M  G W D   R + TY+S++ 
Sbjct: 439 FAG-PLPGMDAEVFDDQGKTVRGEV-GELVLRQPW-VGMTSGFWQD-ARRYEDTYWSRWP 494

Query: 503 SLYYPGDFAMVDEDGYIWVLGRADETLKIAAHRIGAGEVESAITSHPSVAEAAVIGVPDS 562
             +  GD+ +VDE G  ++ GR+D+TLKIA  R+G  E+ES +  HPSV EAA IGVPD+
Sbjct: 495 KTWLHGDWVIVDEGGQWFITGRSDDTLKIAGKRLGPAEMESVLVDHPSVIEAATIGVPDA 554

Query: 563 VKGEEVHAFVVLKQGYAPSSELAKDIQSHVRKVMGPIVSP-QIHFVDKLPKTRSGKVMRR 621
            KGE    FVV++        L +++   V + MG  + P ++H VD+LPKTR+GK++RR
Sbjct: 555 DKGESAVCFVVVRGDGEEVQSLTEELVRFVGERMGKALKPKRVHIVDELPKTRNGKILRR 614

Query: 622 VIKAVMMGSSAGDLTTIEDEASMDEIKK 649
           VI+A  +G +AGDL+++E+  ++++I++
Sbjct: 615 VIRAAYLGENAGDLSSLENAHAVEKIRR 642


Lambda     K      H
   0.318    0.135    0.408 

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: 1197
Number of extensions: 72
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: 661
Length of database: 646
Length adjustment: 38
Effective length of query: 623
Effective length of database: 608
Effective search space:   378784
Effective search space used:   378784
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 54 (25.4 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