GapMind for catabolism of small carbon sources

 

Aligments for a candidate for bch in Marinobacter adhaerens HP15

Align 3-hydroxyisobutyryl-CoA hydrolase (EC 3.1.2.4) (characterized)
to candidate GFF3468 HP15_3410 enoyl-CoA hydratase/isomerase family protein

Query= reanno::pseudo1_N1B4:Pf1N1B4_4790
         (356 letters)



>lcl|FitnessBrowser__Marino:GFF3468 HP15_3410 enoyl-CoA
           hydratase/isomerase family protein
          Length = 367

 Score =  239 bits (609), Expect = 1e-67
 Identities = 139/361 (38%), Positives = 200/361 (55%), Gaps = 13/361 (3%)

Query: 3   ATQNEVLAEVRNHIGHLTLNRPAGLNAITLDMVRSLQQQLDAWAQDPQVHAVVLRGAGEK 62
           + + E LA    H+G LTLN P  LNA++  M+  +Q  LD WA D ++  VV++GAGE+
Sbjct: 2   SVEAEELACREGHMGVLTLNSPGTLNALSEHMIEQIQDILDRWANDDRICIVVIQGAGER 61

Query: 63  AFCAGGDIRSLYDSFKSGDTLHED--FFVEEYALDLAIHHYRKPVLALMDGFVLGGGMGL 120
           AFCAGGDIR LYD+   G    +   FF  EY +D  IH + KPVL +  G V+GGG+G+
Sbjct: 62  AFCAGGDIRELYDAILDGQEPEKPVRFFSREYRMDYNIHRFPKPVLGIAHGVVMGGGLGV 121

Query: 121 VQGADLRVVTERSRLAMPEVAIGYFPDVGGSHFLPRVPGELGIYLGVSGVQIRAADALYC 180
             G   R+VT    LAMPE+ IG FPDVG S FL R+PG LG+++G++G ++  +D L  
Sbjct: 122 FSGCRYRLVTPDVTLAMPEITIGLFPDVGASWFLKRLPGRLGLFMGLTGARLNVSDTLRV 181

Query: 181 GLADWYLESNKLGTLDEQLDQLQWHETPLKDLQGLLAKLAVQQ------LPAAPLAALRP 234
           GLAD  +       L ++L   +W      D   L   L   Q      LP + LA    
Sbjct: 182 GLADMAILPEDRDRLLDRLASERWTGQTAADDNRLFRLLNQIQTPDYRTLPPSHLARHEQ 241

Query: 235 AIDHFFALPDVPSMVEQLRAVTVADSHEWATATADLLESRSPLAMGVTLEMLRRGRHLSL 294
            I    A  ++P +V+QL A  V    +W  A  + L +  P++  +    L++ + +SL
Sbjct: 242 RIARLSAGDELPDIVDQLLAAEV--DCDWWHACMNTLRNGCPVSAWLVWTQLQKAQQMSL 299

Query: 295 EQCFALELHLDRQWFERGDLIEGVRALLIDKDKNPRWSPPTLQALDAGHVASFFTGFDPS 354
           +  F +EL +  +   R DL EG+RAL IDKD+ P+WS P++  +    VA+ FT   P 
Sbjct: 300 KDAFRMELAMVSECIRRPDLTEGIRALAIDKDRQPKWSYPSVADVPEDVVAAHFT---PE 356

Query: 355 W 355
           W
Sbjct: 357 W 357


Lambda     K      H
   0.322    0.138    0.422 

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: 387
Number of extensions: 17
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: 356
Length of database: 367
Length adjustment: 29
Effective length of query: 327
Effective length of database: 338
Effective search space:   110526
Effective search space used:   110526
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 (21.9 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Sep 17 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 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