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

GapMind for catabolism of small carbon sources

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

Align long-chain-3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.211) (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= BRENDA::P40939
         (763 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1850
          Length = 715

 Score =  368 bits (945), Expect = e-106
 Identities = 247/724 (34%), Positives = 377/724 (52%), Gaps = 31/724 (4%)

Query: 42  NYGVKGDVAVVRINSPNSKVNTLSKELHSEFSEVMNEIWASDQIRSAVLISSKPGCFIAG 101
           NY    D  V         VN +++      +  +N +   + +   V+ S+K   F AG
Sbjct: 5   NYEKDADGIVTVTMDMPGPVNAMNQLYRETMAATVNRLEQENGLTGVVIASAK-STFFAG 63

Query: 102 ADINMLAACKTLQEVTQLS--QEAQRIVEKLEKSTKPIVAAINGSCLGGGLEVAISCQYR 159
            D+N L   K   E    +  +  +  + +LE+   P+VAAING+ LGGG E+A++C YR
Sbjct: 64  GDLNELTDFKPGDEADFQAKIELTKNDLRRLERLPVPVVAAINGAALGGGFEIALACNYR 123

Query: 160 IATKDRKTVLGTPEVLLGALPGAGGTQRLPKMVGVPAALDMMLTGRSIRADRAKKMGLVD 219
           +       V+G PEV LG LPG GG  RL   +G+  AL ++L G+ ++   A  +GLV+
Sbjct: 124 VLLNSPAAVVGLPEVSLGLLPGGGGIVRLVHHLGLERALPLLLEGKRMKPAEALALGLVN 183

Query: 220 QLVEPLGPGLKPPEERTIEYLEEVAITFAKGLADKKISPKRDKGLVEKLTAYAMTIPFVR 279
           +L+E     L P  +  I+           G     + P   KG   K+       P V 
Sbjct: 184 ELIEQ-ADALVPAAKAWIKA--------QVGDDGVSLQPWDHKG--HKIPGGTAQQPHVA 232

Query: 280 QQVYKKVEEKVRKQTKGLYPAPLKIIDVVKTGIEQGSDAGYLCESQKFGELVMTKESKAL 339
           Q +    +    K T+GL PAP +I+ V         DA  L E++    L  + ++K +
Sbjct: 233 QMI-AGAQAMTAKNTRGLLPAPERILAVAVEATLLDFDAALLVETRGLTHLAASVQAKNI 291

Query: 340 MGLYHGQVL----CKKNKFGAPQKDVKHLAILGAGLMGAGIAQVSVDKGLKTILKDATLT 395
           +     Q+           G  +  V  L I+GAG+MG GIA VS   G++ +L D +L 
Sbjct: 292 INTMFFQMNEVNGGSSRPTGFDKSKVSKLGIIGAGMMGNGIAHVSAKVGIEVMLLDVSLE 351

Query: 396 ALDRGQQQVFKGLNDKVKKKALTSFERDSIFSNLTGQLDYQGFEKADMVIEAVFEDLSLK 455
           A +RG+  V K L+  V +  L+  ++D I + +   +DY   +  D V+EAVFE + LK
Sbjct: 352 AAERGKANVEKLLSKTVSQGRLSEAKKDEILALIKPTVDYADLQGVDFVVEAVFESVDLK 411

Query: 456 HRVLKEVEAVIPDHCIFASNTSALPISEIAAVSKRPEKVIGMHYFSPVDKMQLLEIITTE 515
            +V ++ EA +P+  +F +NTS LPIS +A  SKRP   IG+H+FSPV++M L+EII  E
Sbjct: 412 GKVTQQAEAQLPESAVFGTNTSTLPISLLANASKRPANFIGIHFFSPVERMPLVEIICGE 471

Query: 516 KTSKDTSASAVAVGLKQGKVIIVVKDGPGFYTTRCLAPMMSEVIRILQEGVDPKKLDSLT 575
           +TS    A A     + GK  IVV D  GF+T+R       E  ++LQEGVDP  +D+L 
Sbjct: 472 QTSDAALAKAFDFARQIGKTAIVVNDSLGFFTSRTFGSYFDEGCKLLQEGVDPLLIDNLG 531

Query: 576 TSFGFPVGAATLVDEVGVDVAKHVAE---DLGKVFGERFGGGNPELLTQMVSKGF--LGR 630
              G PVG  T++DEV +++ + V E   ++G VF   F   + + +  ++ K +   GR
Sbjct: 532 KQIGMPVGPLTVLDEVSLELMRKVNETQKEMG-VFATVFDNSHSDAVGNILIKEYNRPGR 590

Query: 631 KSGKGFYIYQEGVKRKDLNSDMDSILASLKLPPKSEVSSDEDIQFRLVTRFVNEAVMCLQ 690
             G GFY Y EG ++          L  L + P+  V   EDI+ RL+ R V EAV CLQ
Sbjct: 591 HYGGGFYDYPEGGEKTIWPG-----LYELFVRPE-VVLPVEDIKERLLFRQVIEAVKCLQ 644

Query: 691 EGILATPAEGDIGAVFGLGFPPCLGGPFRFVDLYGAQKIVDRLKKYEAAYGKQFTPCQLL 750
           EG+L + A+G++G++ G+G P   GG  +FV+ YG ++ V R ++    YG++FTP  LL
Sbjct: 645 EGVLRSVADGNVGSILGIGAPTWTGGFLQFVNGYGVERFVQRARELAQTYGERFTPPVLL 704

Query: 751 ADHA 754
            + A
Sbjct: 705 LEKA 708


Lambda     K      H
   0.318    0.136    0.385 

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: 1057
Number of extensions: 58
Number of successful extensions: 6
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: 763
Length of database: 715
Length adjustment: 40
Effective length of query: 723
Effective length of database: 675
Effective search space:   488025
Effective search space used:   488025
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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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources