GapMind for catabolism of small carbon sources

 

Aligments for a candidate for ech 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)



>lcl|FitnessBrowser__Marino:GFF1257 HP15_1232 fatty acid oxidation
           complex subunit alpha
          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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 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