GapMind for catabolism of small carbon sources

 

Alignments for a candidate for prpE in Halioglobus japonicus S1-36

Align 4-hydroxybutyrate-CoA ligase (EC 6.2.1.40) (characterized)
to candidate WP_084199459.1 C0029_RS10005 long-chain fatty acid--CoA ligase

Query= BRENDA::A4YDR9
         (549 letters)



>NCBI__GCF_002869505.1:WP_084199459.1
          Length = 511

 Score =  230 bits (586), Expect = 1e-64
 Identities = 160/508 (31%), Positives = 246/508 (48%), Gaps = 28/508 (5%)

Query: 37  DKTAVVYRDSRYTYSTFYDNVMVQASALMRRGFSREDKLSFISRNRPEFLESFFGVPYAG 96
           D+ AVV+ +   TY+ F D V  QA  L   G    D++ ++  N P  LE+ F     G
Sbjct: 23  DRIAVVFEEQEITYAEFADRVRRQAQLLRDAGVCVGDRVGYLGFNHPALLETLFATQALG 82

Query: 97  GVLVPINFRLSPKEMAYIINHSDSKFVVVDEPYLNSLLEVKDQIKAEIILLEDPDNPSAS 156
            + VP+NFRL+ +E+ +IIN +    +VVD+     +    D++        + +     
Sbjct: 83  AIFVPLNFRLTAEELTFIINDAGVHSLVVDDALRPVVEPALDKLCCRRYFSSESEADGWR 142

Query: 157 ETARKEVRMTYRELVKGGSRDPLPIP-AKEEYSMITLYYTSGTTGLPKGVMHHHRGAFLN 215
             + +               +PL    A +++    + YTSGTTGLPKG M  H     N
Sbjct: 143 HLSSERAAC-----------EPLTSTVAVDQHETGLIMYTSGTTGLPKGAMLTHGNFVWN 191

Query: 216 AMAEVLEHQMDLNSVYLWTLPMFHAASWG-FSWATVAVGATNVCLDKVDYPLIYRLVEKE 274
            +   +      +++ L   P+FH       +  +  +G+  V L   D   +    E+ 
Sbjct: 192 NINASMAFGASRDNIILTAAPLFHIGGLNVMTLHSFHLGSKLVLLRNFDPAAVLENFERY 251

Query: 275 RVTHMCAAPTVYVNLADYMKRNNLKFSNRVHMLVAGAAPAPATL-KAMQEIGGYMCHVYG 333
           +VTHM  AP +Y+ +A   +  +   S+ + +LV GAAP P +L +     G   C  YG
Sbjct: 252 KVTHMFGAPAMYLFMAQLPQFADTDLSS-LDVLVCGAAPVPESLIETYGARGVSFCQGYG 310

Query: 334 LTETYGPHSICEWRREWDSLPLEEQAKLKARQGIPYVSFEMDVFDANGKPVPWDGKTIGE 393
           LTET  P S           P    +KL +   +P  S    + DA+ +P+P   K  GE
Sbjct: 311 LTET-APFSAL-------LTPEHAVSKLGSAGQVPLYSGTR-IVDADNQPLPAGEK--GE 359

Query: 394 VVMRGHNVALGYYKNPEKTAESF-RDGWFHSGDAAVVHPDGYIEIVDRFKDLINTGGEKV 452
           + +RG N+  GY+  PE TA +   +GWFHSGD   +  +G++ I DR KD++ +GGE V
Sbjct: 360 ICLRGPNIMKGYWNRPEATASAIDSEGWFHSGDIGYLDDEGFLYICDRLKDMVISGGENV 419

Query: 453 SSILVEKTLMEIPGVKAVAVYGTPDEKWGEVVTARIELQEGVKLTEEEVIKFCKERLAHF 512
               VE  L +   +  VAV GTPDEKWGE VTA + L EG  LT E + +F    LA +
Sbjct: 420 YPAEVEGVLYKHEAIAEVAVIGTPDEKWGEAVTAVVALHEGASLTLEGLREFADPFLARY 479

Query: 513 ECPKIVE-FGPIPMTATGKMQKYVLRNE 539
           + P  +E    +P    GK+ K+VL+ +
Sbjct: 480 KLPLRMEVVEALPRNPAGKVLKFVLKEQ 507


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: 666
Number of extensions: 31
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: 549
Length of database: 511
Length adjustment: 35
Effective length of query: 514
Effective length of database: 476
Effective search space:   244664
Effective search space used:   244664
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 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