GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaH in Methylocystis bryophila S285

Align fatty acid oxidation complex subunit alpha; EC 1.1.1.35; EC 4.2.1.17; EC 5.1.2.3 (characterized)
to candidate WP_085772004.1 B1812_RS13170 3-hydroxyacyl-CoA dehydrogenase NAD-binding domain-containing protein

Query= CharProtDB::CH_003230
         (714 letters)



>NCBI__GCF_002117405.1:WP_085772004.1
          Length = 728

 Score =  405 bits (1041), Expect = e-117
 Identities = 257/728 (35%), Positives = 374/728 (51%), Gaps = 34/728 (4%)

Query: 7   FTLNVRLDNIAVITIDVPGEKMNTLKAEFASQVRAIIKQLRENKELRGVVFVSAKPDNFI 66
           F  +V  D +A++T D+PG  MN +  E  S++  +++++  +  ++G V  S K + F 
Sbjct: 6   FRFDVGADGVALLTWDMPGRSMNVITEEVMSELAQVVEKVAADAAIKGCVIASGK-NAFS 64

Query: 67  AGADINMIGNC----------KTAQEAEAL----ARQGQQLMAEIHALPIQVIAAIHGAC 112
            GAD++M+             K A+EA  L    AR+  QL   +         AIHG C
Sbjct: 65  GGADLSMLQKSRAAHGKALGEKGAEEANRLFFESARKLSQLYRRLETCGKPFAIAIHGVC 124

Query: 113 LGGGLELALACHGRVCTDDPKTVLGLPEVQLGLLPGSGGTQRLPRLIGVSTALEMILTGK 172
           LGG  ELALACH RV  DD KT +GLPEV++GL PG+GGTQR+ R++    AL+ +  G+
Sbjct: 125 LGGAFELALACHHRVLADDDKTKVGLPEVKVGLFPGAGGTQRVARIMPTGDALQFLFKGE 184

Query: 173 QLRAKQALKLGLVDDVVPHSILLEAAVELAKKERPSSRPLPVRERILAGPLGRA------ 226
           QL  K A   GL  ++ P S ++  A +       +  P   ++     P GR       
Sbjct: 185 QLSGKAAKAAGLAQELAPQSEIVSRAKDWILGGGKAIAPWDQKD--FKPPSGRIFSPGGM 242

Query: 227 LLFKMVGKKTEHKTQGNYPATERILEVVETGLAQGTSSGYDAEARAFGELAMTPQSQAL- 285
           +++         +T  NYPA + IL  V  GL      G   EAR F  +  + ++ A+ 
Sbjct: 243 MIWMPANAIYRRETYDNYPAVKAILHCVYEGLQLPIDQGLTVEARWFAHILRSKEAAAMI 302

Query: 286 RSIFFASTDVKKDPG--SDAPPAPLNSVGILGGGLMGGGIAYVTACKAGIPVRIKDINPQ 343
           RS+F +  ++ K      D PP  L  +G+LG G MG G+ YV+A   G+ V + D + +
Sbjct: 303 RSLFLSKNELDKGARRPKDEPPTQLKKIGVLGAGFMGAGVGYVSALN-GLEVVLIDRDQE 361

Query: 344 GINHALKYSWDQLEGKVRRRHLKASERDKQLALISGTTDYRGFAHRDLIIEAVFENLELK 403
             +         + G+V R    AS ++  LA +  T DY      DLI+EAVFE+  +K
Sbjct: 362 SADKGKATIDKLISGQVSRGKATASAKEALLARVEATPDYERLKGCDLILEAVFEDRAVK 421

Query: 404 QQMVAEVEQNCAAHTIFASNTSSLPIGDIAAHATRPEQVIGLHFFSPVEKMPLVEIIPHA 463
            +     +       +FASNTS+LPI  +A  + +PE  IG+HFFSPVEKM LVEII   
Sbjct: 422 AEATKRAQAAVGPDVVFASNTSTLPITSLAETSLKPENFIGVHFFSPVEKMLLVEIILGE 481

Query: 464 GTSAQTIATTVKLAKKQGKTPIVVRDKAGFYVNRILAPYINEAIRMLTQGERVEHIDAAL 523
            TS + +AT +   +   KTPIVV D  GF+ NR +  Y+ E   ML +G     I+ A 
Sbjct: 482 KTSDKALATALDFVRMIKKTPIVVNDSRGFFANRCVLAYVREGQTMLVEGVPPAMIENAA 541

Query: 524 VKFGFPVGPIQLLDEVGIDTGTKIIPVLEAAYGERFSAPA--NVVSSIL-NDDRKGRKNG 580
              G PVGP+ L DEVG+D G KI+   +   G     PA   V+  ++  + R GRKNG
Sbjct: 542 RMAGMPVGPLSLNDEVGLDLGWKILQATKKDLGAAAVDPAQERVLGFLVEKNGRFGRKNG 601

Query: 581 RGFYLYGQKGRKSKKQVDPAIYPLI-GTQGQGRISAPQVAERCVMLMLNEAVRCVDEQVI 639
           +GFY Y   G   KK + P +  L   T     I   ++  R ++    EA R   E V+
Sbjct: 602 KGFYDYPASG---KKTLWPGLAGLAEKTLDPDAIDVKELERRFLVAQAVEAARTFAEHVV 658

Query: 640 RSVRDGDIGAVFGIGFPPFLGGPFRYIDSLGAGEVVAIMQRLATQYGSRFTPCERLVEMG 699
              R+ D+G++ G GF PF GG   YID +G    VA+   LA +YG RF P + L +M 
Sbjct: 659 TDPREADVGSILGFGFAPFTGGALSYIDGMGLKAFVALCDTLAAKYGPRFAPPQLLRDMA 718

Query: 700 ARGESFWK 707
             GE+F++
Sbjct: 719 REGETFYR 726


Lambda     K      H
   0.319    0.137    0.393 

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: 1019
Number of extensions: 52
Number of successful extensions: 9
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: 714
Length of database: 728
Length adjustment: 40
Effective length of query: 674
Effective length of database: 688
Effective search space:   463712
Effective search space used:   463712
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 (21.8 bits)
S2: 55 (25.8 bits)

This GapMind analysis is from Apr 09 2024. 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