GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaH in Pseudomonas fluorescens FW300-N2E2

Align fatty acid oxidation complex α subunit (EC 1.1.1.35; EC 4.2.1.17) (characterized)
to candidate Pf6N2E2_1850 Enoyl-CoA hydratase [isoleucine degradation] (EC 4.2.1.17) / 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35) / 3-hydroxybutyryl-CoA epimerase (EC 5.1.2.3)

Query= metacyc::MONOMER-17591
         (715 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1850
          Length = 715

 Score =  365 bits (937), Expect = e-105
 Identities = 254/715 (35%), Positives = 371/715 (51%), Gaps = 31/715 (4%)

Query: 16  GIVELNFDLKGESVNKFNRLTLSELRAAVDAIKADASVKGVIVTSGKDVFIVGADITEFV 75
           GIV +  D+ G  VN  N+L    + A V+ ++ +  + GV++ S K  F  G D+ E  
Sbjct: 12  GIVTVTMDMPGP-VNAMNQLYRETMAATVNRLEQENGLTGVVIASAKSTFFAGGDLNELT 70

Query: 76  DNFQLPDEELMAGNLEANKI-FSDFEDLDVPTVAAINGIALGGGLEMCLAADFRVM--SA 132
           D F+  DE      +E  K      E L VP VAAING ALGGG E+ LA ++RV+  S 
Sbjct: 71  D-FKPGDEADFQAKIELTKNDLRRLERLPVPVVAAINGAALGGGFEIALACNYRVLLNSP 129

Query: 133 TAKVGLPEVKLGIYPGFGGTVRLPRLIGCDNAVEWIASGKENKAEDALKVGAVDAVVAPE 192
            A VGLPEV LG+ PG GG VRL   +G + A+  +  GK  K  +AL +G V+ ++   
Sbjct: 130 AAVVGLPEVSLGLLPGGGGIVRLVHHLGLERALPLLLEGKRMKPAEALALGLVNELIEQA 189

Query: 193 QLQAAALDLAKRAVAGE-------LDHKARRQPKLEKLKLNAIEQMMAFETAKGFVAGQA 245
                A     +A  G+        DHK  + P     + + + QM+A   A+   A   
Sbjct: 190 DALVPAAKAWIKAQVGDDGVSLQPWDHKGHKIPGGTAQQPH-VAQMIA--GAQAMTAKNT 246

Query: 246 GPNYPAPVEAIKSIQKAANFGRDKALEVEAAGFVKLAKTSVAQSLIG-LFLNDQELKKKA 304
               PAP   +    +A     D AL VE  G   LA +  A+++I  +F    E+   +
Sbjct: 247 RGLLPAPERILAVAVEATLLDFDAALLVETRGLTHLAASVQAKNIINTMFFQMNEVNGGS 306

Query: 305 KKYDEVAKD-VKLAAVLGAGIMGGGIAYQSALKGTPILMKDIREEGIQMGLNEAAKLLGK 363
            +     K  V    ++GAG+MG GIA+ SA  G  +++ D+  E  + G     KLL K
Sbjct: 307 SRPTGFDKSKVSKLGIIGAGMMGNGIAHVSAKVGIEVMLLDVSLEAAERGKANVEKLLSK 366

Query: 364 RVEKGRLTPAKMAEALNGIRPTMSYGDFGNVDIVVEAVVENPKVKQAVLAEVEGAVKEDA 423
            V +GRL+ AK  E L  I+PT+ Y D   VD VVEAV E+  +K  V  + E  + E A
Sbjct: 367 TVSQGRLSEAKKDEILALIKPTVDYADLQGVDFVVEAVFESVDLKGKVTQQAEAQLPESA 426

Query: 424 IIASNTSTISISLLAQALKRPENFCGMHFFNPVHMMPLVEVIRGEKTGETAIATTVAYAK 483
           +  +NTST+ ISLLA A KRP NF G+HFF+PV  MPLVE+I GE+T + A+A    +A+
Sbjct: 427 VFGTNTSTLPISLLANASKRPANFIGIHFFSPVERMPLVEIICGEQTSDAALAKAFDFAR 486

Query: 484 KMGKSPIVVNDCPGFLVNRVLFPYFGGFAKLLSFGVDFVRIDKVMEKFGWPMGPAYLSDV 543
           ++GK+ IVVND  GF  +R    YF    KLL  GVD + ID + ++ G P+GP  + D 
Sbjct: 487 QIGKTAIVVNDSLGFFTSRTFGSYFDEGCKLLQEGVDPLLIDNLGKQIGMPVGPLTVLDE 546

Query: 544 VGIDTGHHGRDVMAE--GFPDRMAVEGKTAVD--VMYEANRLGQKNGKGFYAYETDKRGK 599
           V ++      +   E   F          AV   ++ E NR G+  G GFY Y       
Sbjct: 547 VSLELMRKVNETQKEMGVFATVFDNSHSDAVGNILIKEYNRPGRHYGGGFYDYPEG---- 602

Query: 600 PKKVTDPQAYEV-LKPIVVEQREVTDEDIVNFMMIPLCLETVRCLEDGIVETAAEADMGL 658
            +K   P  YE+ ++P VV    +  EDI   ++    +E V+CL++G++ + A+ ++G 
Sbjct: 603 GEKTIWPGLYELFVRPEVV----LPVEDIKERLLFRQVIEAVKCLQEGVLRSVADGNVGS 658

Query: 659 IYGIGFPPFRGGALRYIDSIGVAEFVALADKYAE-LGALYHPTAKLREMAKNGQK 712
           I GIG P + GG L++++  GV  FV  A + A+  G  + P   L E A  G++
Sbjct: 659 ILGIGAPTWTGGFLQFVNGYGVERFVQRARELAQTYGERFTPPVLLLEKAAKGEE 713


Lambda     K      H
   0.318    0.137    0.388 

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: 1100
Number of extensions: 48
Number of successful extensions: 5
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: 715
Length of database: 715
Length adjustment: 39
Effective length of query: 676
Effective length of database: 676
Effective search space:   456976
Effective search space used:   456976
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 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