GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__pseudo6_N2E2: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)
          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 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