GapMind for Amino acid biosynthesis

 

Alignments for a candidate for prpE in Cupriavidus basilensis 4G11

Align 4-hydroxybutyrate-CoA ligase (EC 6.2.1.40) (characterized)
to candidate RR42_RS27915 RR42_RS27915 acyl-CoA synthetase

Query= BRENDA::A4YDR9
         (549 letters)



>FitnessBrowser__Cup4G11:RR42_RS27915
          Length = 545

 Score =  390 bits (1003), Expect = e-113
 Identities = 215/530 (40%), Positives = 306/530 (57%), Gaps = 14/530 (2%)

Query: 22  LTPLLFLERAGKYFKDKTAVVYRDSRYTYSTFYDNVMVQASALMRRGFSREDKLSFISRN 81
           LTP+ FL RA   + D+ A+V+   R  +   Y      AS L   G  + D ++ +  N
Sbjct: 19  LTPIDFLARAASVYGDRLAIVHGPVRQNWRDTYARARRLASGLASLGVGKGDTVAALLPN 78

Query: 82  RPEFLESFFGVPYAGGVLVPINFRLSPKEMAYIINHSDSKFVVVDEPYLNSLLEVKDQIK 141
            P  +E+ FGVP AG VL  +N RL    + +++ H +++ ++ D  + +   ++ ++I 
Sbjct: 79  TPAMVEAHFGVPMAGAVLNALNIRLDASNLIFMLRHGEARVLLADTEFADVARQIANEIP 138

Query: 142 -----AEIILLEDPDNPSASETARKEVRMTYRELVKGGSRDPLPIPAKEEYSMITLYYTS 196
                A +  L   D P+  ET  +      R L  G       +PA +E+  I L YTS
Sbjct: 139 GLKVVAVLDALGPQDAPAFGETDYE------RLLASGDPEFAWQMPA-DEWDAIALNYTS 191

Query: 197 GTTGLPKGVMHHHRGAFLNAMAEVLEHQMDLNSVYLWTLPMFHAASWGFSWATVAVGATN 256
           GTTG PKGV++HHRGA +NA++ +LE  +  ++VYLWTLPMFH   W F W   A    N
Sbjct: 192 GTTGDPKGVVYHHRGAAINAISNILEWDLPKHAVYLWTLPMFHCNGWCFPWTIAARAGVN 251

Query: 257 VCLDKVDYPLIYRLVEKERVTHMCAAPTVYVNLADYMKRNNLKFSNRVHMLVAGAAPAPA 316
           VCL K +  L++ L+  E VTH CAAP V+  L +            V  +VAGA P  A
Sbjct: 252 VCLRKFEPKLVFDLMRDEGVTHYCAAPIVHTALVNAPLAWRDGVRGPVRGMVAGAPPPAA 311

Query: 317 TLKAMQEIGGYMCHVYGLTETYGPHSICEWRREWDSLPLEEQAKLKARQGIPY-VSFEMD 375
            L  M+ +G  + HVYGLTETYGP ++C  + +W SL  E++A  KARQG+ Y +  E+ 
Sbjct: 312 VLAQMEAMGFALTHVYGLTETYGPAAVCAEQDDWASLSQEDRATKKARQGVRYHLQTEVA 371

Query: 376 VFDANG-KPVPWDGKTIGEVVMRGHNVALGYYKNPEKTAESFRDGWFHSGDAAVVHPDGY 434
           V D +  +PV  DG+ IGE++ RG+    GY KN + T E+F  GWFH+GD  V  PDGY
Sbjct: 372 VLDPDTMQPVASDGEEIGEIMFRGNICMKGYLKNEKATREAFAGGWFHTGDLGVCTPDGY 431

Query: 435 IEIVDRFKDLINTGGEKVSSILVEKTLMEIPGVKAVAVYGTPDEKWGEVVTARIELQEGV 494
           ++I DR KD+I +GGE +SS+ VE  +   P V AVAV   PD KWGE   A +EL++G 
Sbjct: 432 VKIKDRSKDIIISGGENISSVEVEDAIYRHPAVLAVAVVAQPDVKWGETPCAFVELKDGA 491

Query: 495 KLTEEEVIKFCKERLAHFECPKIVEFGPIPMTATGKMQKYVLRNEAKAKA 544
             T +E+I  C+  LA F+ PK V FGP+P T+TGK+QK+ LR + K+ A
Sbjct: 492 SATADELIAHCRTLLAGFKVPKAVYFGPLPKTSTGKIQKFELRKKVKSDA 541


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: 764
Number of extensions: 31
Number of successful extensions: 4
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: 545
Length adjustment: 36
Effective length of query: 513
Effective length of database: 509
Effective search space:   261117
Effective search space used:   261117
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 Aug 03 2021. The underlying query database was built on Aug 03 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