GapMind for catabolism of small carbon sources

 

Aligments for a candidate for prpE in Paraburkholderia bryophila 376MFSha3.1

Align 4-hydroxybutyrate-CoA ligase (EC 6.2.1.40) (characterized)
to candidate H281DRAFT_05558 H281DRAFT_05558 fatty-acyl-CoA synthase

Query= BRENDA::A4YDR9
         (549 letters)



>lcl|FitnessBrowser__Burk376:H281DRAFT_05558 H281DRAFT_05558
           fatty-acyl-CoA synthase
          Length = 550

 Score =  405 bits (1041), Expect = e-117
 Identities = 223/532 (41%), Positives = 309/532 (58%), Gaps = 4/532 (0%)

Query: 8   NYEGVDPTGSWYSVLTPLLFLERAGKYFKDKTAVVYRDSRYTYSTFYDNVMVQASALMRR 67
           N  G+ P  + +  LTP+ FL+RA K F D+TAVVY   R T+          ASAL R 
Sbjct: 7   NDPGLRPRAANFDALTPVTFLQRAEKVFPDRTAVVYGSHRETWREHAATCRRFASALARA 66

Query: 68  GFSREDKLSFISRNRPEFLESFFGVPYAGGVLVPINFRLSPKEMAYIINHSDSKFVVVDE 127
           G    D ++ +  N P  L + F VP AG VL  IN RL  + ++YI+ HS+++ ++VD 
Sbjct: 67  GIEYGDVVALLMTNTPPMLAAHFAVPMAGAVLNTINTRLDAENVSYILGHSEARLIIVDA 126

Query: 128 PYLNSLLEVKDQIKAEIILLEDPDNPSASETARKEVRMTYRELVKGGSRDPLPIPAKEEY 187
            +L        +++    L+   D  +A   A  +V   Y   +  G  +      +EE+
Sbjct: 127 EFLELARTAVARLQHPPRLVCFADEQAAF-AASSDVE-DYVSFLASGDENASFCKVEEEW 184

Query: 188 SMITLYYTSGTTGLPKGVMHHHRGAFLNAMAEVLEHQMDLNSVYLWTLPMFHAASWGFSW 247
           + I + YTSGTTG PKGV++ HRGA+L+A++ ++   +   + YLWTLP+FH   W   W
Sbjct: 185 TPIAVNYTSGTTGRPKGVVYSHRGAYLSAVSSIISWGVPKAASYLWTLPLFHCNGWCMPW 244

Query: 248 ATVAVGATNVCLDKVDYPLIYRLVEKERVTHMCAAPTVYVNLADYMKRNNLKFSNRVHML 307
                G  +VCL +VD   I +L+  ERVTH C AP V+  + D  ++ +L F+  V  L
Sbjct: 245 VLALQGGKSVCLRRVDGDKIVQLINDERVTHYCGAPIVHALIRDRAQQQDLVFNPAVSAL 304

Query: 308 VAGAAPAPATLKAMQEIGGYMCHVYGLTETYGPHSICEWRREWDSLPLEEQAKLKARQGI 367
           + GA P  + + AM  IG  + H+YGLTETYGP +ICE +  W  L   E+A  KARQG+
Sbjct: 305 IGGAPPPASLIAAMDAIGVQLTHIYGLTETYGPAAICEQQPAWAELGEAERADRKARQGV 364

Query: 368 PY-VSFEMDVFDANGK-PVPWDGKTIGEVVMRGHNVALGYYKNPEKTAESFRDGWFHSGD 425
            Y +   M V + N    V  DG  +GE+V RG+   +GY K+ E T  +F  GWF SGD
Sbjct: 365 NYALQAGMTVMNCNSSDEVSADGAMMGEIVFRGNMTMMGYLKDSESTDRAFDGGWFRSGD 424

Query: 426 AAVVHPDGYIEIVDRFKDLINTGGEKVSSILVEKTLMEIPGVKAVAVYGTPDEKWGEVVT 485
            AV+ PDGY+ I DR KD+I +GGE +SS+ VE  L     V A AV   PDEKWGEV  
Sbjct: 425 LAVLEPDGYVRIKDRSKDIIISGGENISSVEVEDVLYRHETVAAAAVVAMPDEKWGEVPV 484

Query: 486 ARIELQEGVKLTEEEVIKFCKERLAHFECPKIVEFGPIPMTATGKMQKYVLR 537
           A +EL+EG   +E+ +I  C+E+LAHF+CPK V F PIP TATGK+QK VLR
Sbjct: 485 AIVELREGSHASEDALIAHCREQLAHFKCPKRVIFHPIPKTATGKIQKNVLR 536


Lambda     K      H
   0.319    0.136    0.411 

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: 731
Number of extensions: 33
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: 549
Length of database: 550
Length adjustment: 36
Effective length of query: 513
Effective length of database: 514
Effective search space:   263682
Effective search space used:   263682
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 Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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