GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fadB in Marinobacter adhaerens HP15

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 GFF1257 HP15_1232 fatty acid oxidation complex subunit alpha

Query= CharProtDB::CH_003230
         (714 letters)



>FitnessBrowser__Marino:GFF1257
          Length = 716

 Score =  381 bits (979), Expect = e-110
 Identities = 258/726 (35%), Positives = 375/726 (51%), Gaps = 37/726 (5%)

Query: 5   SAFTLNVRLDNIAVITIDVPGEKMNTLKAEFASQVRAIIKQLRENKE-LRGVVFVSAKPD 63
           SA    +  D I  +TID+PG+  NT+ A F   +     +++E+ + +RG++  SAK  
Sbjct: 2   SAIRYELGSDQILTLTIDMPGQSANTMNAAFRDALSETAAKVKEDLDNIRGIIIASAKK- 60

Query: 64  NFIAGADINMIGNCKTAQEAEALARQGQQLMAEIHALPIQ---VIAAIHGACLGGGLELA 120
            F AG D+  +    T ++A         L + +  L      V+AAI+G+ LGGGLE+A
Sbjct: 61  TFFAGGDLKELHKV-TREDARTFEDMVNGLKSHMRFLETTGKPVVAAINGSALGGGLEIA 119

Query: 121 LACHGRVCTDDPKTVLGLPEVQLGLLPGSGGTQRLPRLIGVSTALEMILTGKQLRAKQAL 180
           LACH RV  +D    LGLPEV LGLLPG GGTQRLPR+IG+  A   ++ GK++  K AL
Sbjct: 120 LACHYRVAINDDSIQLGLPEVTLGLLPGGGGTQRLPRMIGLEAAFPFLMEGKKVNPKAAL 179

Query: 181 KLGLVDDVVPHSILLEAAVELAKKERPSSRPLPVRE--------RILAG-PLGRALLFKM 231
           K G++++      L ++A ++  K R      P  +        R   G P   A+  K+
Sbjct: 180 KAGIINE------LADSADDMITKARAFIEANPKCQQPWDQKGFRFPGGAPHHPAMAQKL 233

Query: 232 V--GKKTEHKTQGNYPATERILEVVETGLAQGTSSGYDAEARAFGELAMTPQSQALRSIF 289
                  + KT+G YPA ERIL     G      +G   E R F EL +   ++ +   F
Sbjct: 234 AIAPAMLKQKTKGCYPAPERILSAAVEGAQVDFDNGSLIETRYFAELVIGQVAKNMTGTF 293

Query: 290 FASTDVKKDPGS---DAPPAPLNSVGILGGGLMGGGIAYVTACKAGIPVRIKDINPQGIN 346
           +   +  K  GS            VG+LG G+MG GIAY TA + GI V +KD++ +   
Sbjct: 294 WFQLNAIKAGGSRPEGVEKETFRKVGVLGAGMMGAGIAYSTATR-GIDVVLKDVSVENAE 352

Query: 347 HALKYSWDQLEGKVRRRHLKASERDKQLALISGTTDYRGFAHRDLIIEAVFENLELKQQM 406
               YS + L  KV R  +   ++   L+ I  T         DL+IEAVFE+  LK ++
Sbjct: 353 KGKSYSENLLAKKVSRGRMTEEQKADILSRIKATDSSDDLEGCDLVIEAVFEDSGLKAKV 412

Query: 407 VAEVEQNCAAHTIFASNTSSLPIGDIAAHATRPEQVIGLHFFSPVEKMPLVEIIPHAGTS 466
             E E    A+ IFASNTS++PI  +A  +   E  IGLHFFSPV+KM LVEII    TS
Sbjct: 413 TQEAEPKLVANGIFASNTSTIPITQLAGASANAENFIGLHFFSPVDKMQLVEIIVGEKTS 472

Query: 467 AQTIATTVKLAKKQGKTPIVVRDKAGFYVNRILAPYINEAIRMLTQGERVEHIDAALVKF 526
            +T+A +    ++ GK P+VV D  GF+ +R+   ++NE I ML +G     I+ A V  
Sbjct: 473 DETLARSFDYVQQIGKIPVVVNDSRGFFTSRVFGTFVNEGICMLGEGIHPASIENAGVLA 532

Query: 527 GFPVGPIQLLDEVGIDTGTKIIPV----LEAAYGERFSAPAN-VVSSILND-DRKGRKNG 580
           G PVGP+ + DEV +     I        EAA G     PA  V+ +++N+  RKG+  G
Sbjct: 533 GMPVGPLAISDEVSMTLMQHIRDQSRKDTEAAGGTWNPHPAEAVIDAMVNEHGRKGKAAG 592

Query: 581 RGFYLYGQKGRKSKKQVDPAIYPLIGTQGQGR-ISAPQVAERCVMLMLNEAVRCVDEQVI 639
            GFY Y   G   KK + P +  L     + R +   ++ +R + +   E VRC++E V+
Sbjct: 593 AGFYEYPANG---KKHLWPELETLFVNAEKARTVKLQELKDRILFIQAIETVRCLEEGVL 649

Query: 640 RSVRDGDIGAVFGIGFPPFLGGPFRYIDSLGAGEVVAIMQRLATQYGSRFTPCERLVEMG 699
           R+V D +IG++FGIG+ P+ GG  ++I+  G          LA  YG RF P + L E  
Sbjct: 650 RTVEDANIGSIFGIGYAPWTGGAIQFINQYGVRAFTERASALAETYGERFAPPKLLQEKA 709

Query: 700 ARGESF 705
                F
Sbjct: 710 ETNTPF 715


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: 953
Number of extensions: 37
Number of successful extensions: 7
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: 716
Length adjustment: 39
Effective length of query: 675
Effective length of database: 677
Effective search space:   456975
Effective search space used:   456975
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