GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fadB in Pseudomonas putida KT2440

Align FadB (EC 5.3.3.8; EC 1.1.1.35; EC 5.1.2.3; EC 4.2.1.17; EC 1.1.1.36) (characterized)
to candidate PP_2136 PP_2136 enoyl-CoA hydratase/3-hydroxyacyl-CoA dehydrogenase

Query= metacyc::G1G01-2277-MONOMER
         (715 letters)



>FitnessBrowser__Putida:PP_2136
          Length = 715

 Score = 1394 bits (3607), Expect = 0.0
 Identities = 715/715 (100%), Positives = 715/715 (100%)

Query: 1   MIYEGKAITVKALESGIVELKFDLKGESVNKFNRLTLNELRQAVDAIRADASVKGVIVRS 60
           MIYEGKAITVKALESGIVELKFDLKGESVNKFNRLTLNELRQAVDAIRADASVKGVIVRS
Sbjct: 1   MIYEGKAITVKALESGIVELKFDLKGESVNKFNRLTLNELRQAVDAIRADASVKGVIVRS 60

Query: 61  GKDVFIVGADITEFVDNFKLPEAELVAGNLEANRIFNAFEDLEVPTVAAINGIALGGGLE 120
           GKDVFIVGADITEFVDNFKLPEAELVAGNLEANRIFNAFEDLEVPTVAAINGIALGGGLE
Sbjct: 61  GKDVFIVGADITEFVDNFKLPEAELVAGNLEANRIFNAFEDLEVPTVAAINGIALGGGLE 120

Query: 121 MCLAADYRVMSTSARIGLPEVKLGIYPGFGGTVRLPRLIGSDNAIEWIAAGKENRAEDAL 180
           MCLAADYRVMSTSARIGLPEVKLGIYPGFGGTVRLPRLIGSDNAIEWIAAGKENRAEDAL
Sbjct: 121 MCLAADYRVMSTSARIGLPEVKLGIYPGFGGTVRLPRLIGSDNAIEWIAAGKENRAEDAL 180

Query: 181 KVGAVDAVVAPELLLAGALDLIKRAISGELDYKAKRQPKLEKLKLNAIEQMMAFETAKGF 240
           KVGAVDAVVAPELLLAGALDLIKRAISGELDYKAKRQPKLEKLKLNAIEQMMAFETAKGF
Sbjct: 181 KVGAVDAVVAPELLLAGALDLIKRAISGELDYKAKRQPKLEKLKLNAIEQMMAFETAKGF 240

Query: 241 VAGQAGPNYPAPVEAIKSIQKAANFGRDKALEVEAAGFAKLAKTSVAESLIGLFLNDQEL 300
           VAGQAGPNYPAPVEAIKSIQKAANFGRDKALEVEAAGFAKLAKTSVAESLIGLFLNDQEL
Sbjct: 241 VAGQAGPNYPAPVEAIKSIQKAANFGRDKALEVEAAGFAKLAKTSVAESLIGLFLNDQEL 300

Query: 301 KRKAKAHDEIAHDVKQAAVLGAGIMGGGIAYQSAVKGTPILMKDIREEAIQLGLNEASKL 360
           KRKAKAHDEIAHDVKQAAVLGAGIMGGGIAYQSAVKGTPILMKDIREEAIQLGLNEASKL
Sbjct: 301 KRKAKAHDEIAHDVKQAAVLGAGIMGGGIAYQSAVKGTPILMKDIREEAIQLGLNEASKL 360

Query: 361 LGNRVEKGRLTPAKMAEALNAIRPTLSYGDFANVDIVVEAVVENPKVKQAVLAEVEGQVK 420
           LGNRVEKGRLTPAKMAEALNAIRPTLSYGDFANVDIVVEAVVENPKVKQAVLAEVEGQVK
Sbjct: 361 LGNRVEKGRLTPAKMAEALNAIRPTLSYGDFANVDIVVEAVVENPKVKQAVLAEVEGQVK 420

Query: 421 DDAILASNTSTISINLLAKALKRPENFVGMHFFNPVHMMPLVEVIRGEKSSDVAVATTVA 480
           DDAILASNTSTISINLLAKALKRPENFVGMHFFNPVHMMPLVEVIRGEKSSDVAVATTVA
Sbjct: 421 DDAILASNTSTISINLLAKALKRPENFVGMHFFNPVHMMPLVEVIRGEKSSDVAVATTVA 480

Query: 481 YAKKMGKNPIVVNDCPGFLVNRVLFPYFGGFAKLVSAGVDFVRIDKVMEKFGWPMGPAYL 540
           YAKKMGKNPIVVNDCPGFLVNRVLFPYFGGFAKLVSAGVDFVRIDKVMEKFGWPMGPAYL
Sbjct: 481 YAKKMGKNPIVVNDCPGFLVNRVLFPYFGGFAKLVSAGVDFVRIDKVMEKFGWPMGPAYL 540

Query: 541 MDVVGIDTGHHGRDVMAEGFPDRMKDERRSAVDALYEANRLGQKNGKGFYAYETDKRGKP 600
           MDVVGIDTGHHGRDVMAEGFPDRMKDERRSAVDALYEANRLGQKNGKGFYAYETDKRGKP
Sbjct: 541 MDVVGIDTGHHGRDVMAEGFPDRMKDERRSAVDALYEANRLGQKNGKGFYAYETDKRGKP 600

Query: 601 KKVFDATVLDVLKPIVFEQREVTDEDIINWMMVPLCLETVRCLEDGIVETAAEADMGLVY 660
           KKVFDATVLDVLKPIVFEQREVTDEDIINWMMVPLCLETVRCLEDGIVETAAEADMGLVY
Sbjct: 601 KKVFDATVLDVLKPIVFEQREVTDEDIINWMMVPLCLETVRCLEDGIVETAAEADMGLVY 660

Query: 661 GIGFPPFRGGALRYIDSIGVAEFVALADQYADLGPLYHPTAKLREMAKNGQRFFN 715
           GIGFPPFRGGALRYIDSIGVAEFVALADQYADLGPLYHPTAKLREMAKNGQRFFN
Sbjct: 661 GIGFPPFRGGALRYIDSIGVAEFVALADQYADLGPLYHPTAKLREMAKNGQRFFN 715


Lambda     K      H
   0.319    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: 1738
Number of extensions: 57
Number of successful extensions: 1
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 ( 7.4 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