GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaH in Phaeobacter inhibens BS107

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 GFF1187 PGA1_c12020 fatty acid oxidation complex FadJ subunit alpha

Query= CharProtDB::CH_003230
         (714 letters)



>FitnessBrowser__Phaeo:GFF1187
          Length = 733

 Score =  384 bits (987), Expect = e-111
 Identities = 254/730 (34%), Positives = 372/730 (50%), Gaps = 37/730 (5%)

Query: 5   SAFTLNVRLDNIAVITIDVPGEKMNTLKAEFASQVRAIIKQLRENKELRGVVFVSAKPDN 64
           S FT+    D +A+IT D PG+ MN L  +    +  ++     +  ++G+V  S K D 
Sbjct: 2   SDFTMKKDADGVAIITWDCPGKTMNVLNGQAMIDLDGLVDDALADDAVKGIVITSGKKD- 60

Query: 65  FIAGADINMI-----------------GNCKTAQEAEALARQGQQLMAEIHALPIQVIAA 107
           F  G D+N++                 G  K  +    + R G          P  V AA
Sbjct: 61  FAGGMDLNVLAKMKEDAGDEPARGLFEGIMKMHEGLRKIERAGMDPKTNKGGKP--VAAA 118

Query: 108 IHGACLGGGLELALACHGRVCTDDPKTVLGLPEVQLGLLPGSGGTQRLPRLIGVSTALEM 167
           + G  +G GLEL L+ H     D+PK  +GLPE+ +G+ PG+GGT RL R +G   A   
Sbjct: 119 LPGTAVGIGLELPLSTHRIFAADNPKAKIGLPEIMVGIFPGAGGTTRLVRKMGAMAAAPF 178

Query: 168 ILTGKQLRAKQALKLGLVDDVVPHSILLEAAVELAKKERPSSRPLPVRERILAG-----P 222
           +L GK +  K+A   G++D+VV   +    A  L  K+    +P   +   + G     P
Sbjct: 179 LLEGKLVDPKKAKGAGIIDEVVEDPLAAARAWVLEAKDADIVKPWDAKGYKMPGGAPYHP 238

Query: 223 LGRALLFKMVGKKTEHKTQGNYPATERILEVVETGLAQGTSSGYDAEARAFGELAMTPQS 282
            G  + F         KT G +PA + +L  V  G      +    EAR F  + M P S
Sbjct: 239 AG-FMTFLGAAAMVHGKTFGAFPAAKALLSAVYEGALVPFDTALKIEARWFTHVLMNPSS 297

Query: 283 QAL-RSIFFASTDVKKDPGSDA--PPAPLNSVGILGGGLMGGGIAYVTACKAGIPVRIKD 339
           +A+ RS+F     ++K     A      +  +G+LG G+MG GIA V+A +AG+ V + D
Sbjct: 298 EAMIRSLFLNKEALEKGAVRPAGIEDQSVKKIGVLGAGMMGAGIALVSA-QAGMEVVLID 356

Query: 340 INPQGINHALKYSWDQLEGKVRRRHLKASERDKQLALISGTTDYRGFAHRDLIIEAVFEN 399
            +    +    Y+   L+  ++R  + A +++  L+ I+ T D       DLIIEAVFE+
Sbjct: 357 RDQAAADKGKAYTESYLDKGIKRGKVTADKKEAMLSRITATPDLDHLKGCDLIIEAVFED 416

Query: 400 LELKQQMVAEVEQNCAAHTIFASNTSSLPIGDIAAHATRPEQVIGLHFFSPVEKMPLVEI 459
             +K +M  +VE       IFASNTS+LPI D+A  + RPEQ IG+HFFSPVEKM LVEI
Sbjct: 417 PGVKAEMTKKVEAIIPEDCIFASNTSTLPITDLAEASVRPEQFIGIHFFSPVEKMFLVEI 476

Query: 460 IPHAGTSAQTIATTVKLAKKQGKTPIVVRDKAGFYVNRILAPYINEAIRMLTQGERVEHI 519
           I    T  + +A  +   ++  KTPIVV D   FY NR + PY+NE  RM+T+G     I
Sbjct: 477 IKGEKTGDRAVAKALDYVRQIRKTPIVVNDARFFYCNRCIIPYVNEGARMITEGVAPALI 536

Query: 520 DAALVKFGFPVGPIQLLDEVGIDTGTKIIPVLEAAYGERF--SAPANVVSSILNDDRKGR 577
           D A  + GFPVGPIQL DE  ID G KI    +AA G+ +  SA  +++  +    R GR
Sbjct: 537 DNAARQLGFPVGPIQLTDETSIDLGAKIARATKAAMGDAYPESAADDLIFWMEEQGRLGR 596

Query: 578 KNGRGFYLYGQKG-RKSKKQVDPAIYPLIGTQGQGRISAPQVAERCVMLMLNEAVRCVDE 636
           K+  GF+ Y  KG R+   +     YPL   Q        +V ER +   + EAVR ++E
Sbjct: 597 KSNAGFFDYDDKGKRQGYWKGMQEKYPLADEQP----DLIEVQERLMFAQVLEAVRALEE 652

Query: 637 QVIRSVRDGDIGAVFGIGFPPFLGGPFRYIDSLGAGEVVAIMQRLATQYGSRFTPCERLV 696
            V+  +R+GD+GA+   GF P+ GGP  ++D +G         +L  +YG RFT    L 
Sbjct: 653 GVLMDIREGDVGAILAWGFAPWSGGPLSWLDIIGTPYAAERCDQLTAKYGERFTCPPLLR 712

Query: 697 EMGARGESFW 706
           EM  +G++F+
Sbjct: 713 EMAEKGQTFY 722


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: 1084
Number of extensions: 53
Number of successful extensions: 8
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: 733
Length adjustment: 40
Effective length of query: 674
Effective length of database: 693
Effective search space:   467082
Effective search space used:   467082
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 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:

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