GapMind for catabolism of small carbon sources

 

Aligments for a candidate for put1 in Echinicola vietnamensis KMM 6221, DSM 17526

Align Proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate Echvi_0119 Echvi_0119 Proline dehydrogenase

Query= reanno::Cola:Echvi_0119
         (398 letters)



>lcl|FitnessBrowser__Cola:Echvi_0119 Echvi_0119 Proline
           dehydrogenase
          Length = 398

 Score =  790 bits (2041), Expect = 0.0
 Identities = 398/398 (100%), Positives = 398/398 (100%)

Query: 1   MNTKPNISFENTEIAFASRTDAELRKMYLFFAVMDKNWAVKIGTNLSAVAFKLKLPVKGI 60
           MNTKPNISFENTEIAFASRTDAELRKMYLFFAVMDKNWAVKIGTNLSAVAFKLKLPVKGI
Sbjct: 1   MNTKPNISFENTEIAFASRTDAELRKMYLFFAVMDKNWAVKIGTNLSAVAFKLKLPVKGI 60

Query: 61  MKKTIFGHFCGGESVEDCSKSIQELQEFGIGTILDYSVEGTGTEKSYDFTRDEILRTIER 120
           MKKTIFGHFCGGESVEDCSKSIQELQEFGIGTILDYSVEGTGTEKSYDFTRDEILRTIER
Sbjct: 61  MKKTIFGHFCGGESVEDCSKSIQELQEFGIGTILDYSVEGTGTEKSYDFTRDEILRTIER 120

Query: 121 SAGASEIPFSVFKVTGLGSYKIMTKVQAGQKLSAKEQEAFERLKDRVDTLCKAAYENDVR 180
           SAGASEIPFSVFKVTGLGSYKIMTKVQAGQKLSAKEQEAFERLKDRVDTLCKAAYENDVR
Sbjct: 121 SAGASEIPFSVFKVTGLGSYKIMTKVQAGQKLSAKEQEAFERLKDRVDTLCKAAYENDVR 180

Query: 181 IMIDGEESWFQDVIDDMAYEAMEKYNKEKAIVYNTFQMYRKDMLGLLKKAHEEAELKGYH 240
           IMIDGEESWFQDVIDDMAYEAMEKYNKEKAIVYNTFQMYRKDMLGLLKKAHEEAELKGYH
Sbjct: 181 IMIDGEESWFQDVIDDMAYEAMEKYNKEKAIVYNTFQMYRKDMLGLLKKAHEEAELKGYH 240

Query: 241 VGAKLVRGAYMEKERDRAEDRGYPSPIQDTKEDTDNAYNDALKFSMEHKDRIYLVSGSHN 300
           VGAKLVRGAYMEKERDRAEDRGYPSPIQDTKEDTDNAYNDALKFSMEHKDRIYLVSGSHN
Sbjct: 241 VGAKLVRGAYMEKERDRAEDRGYPSPIQDTKEDTDNAYNDALKFSMEHKDRIYLVSGSHN 300

Query: 301 ELSNIILTELMNLHGVAANDKRVYFSQLYGMSDNISYNLAFAGYNVAKYVPYGPVESVMP 360
           ELSNIILTELMNLHGVAANDKRVYFSQLYGMSDNISYNLAFAGYNVAKYVPYGPVESVMP
Sbjct: 301 ELSNIILTELMNLHGVAANDKRVYFSQLYGMSDNISYNLAFAGYNVAKYVPYGPVESVMP 360

Query: 361 YLYRRASENTSVAGQSSREFELIKNEMARRASLKKTII 398
           YLYRRASENTSVAGQSSREFELIKNEMARRASLKKTII
Sbjct: 361 YLYRRASENTSVAGQSSREFELIKNEMARRASLKKTII 398


Lambda     K      H
   0.316    0.132    0.371 

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: 776
Number of extensions: 17
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: 398
Length of database: 398
Length adjustment: 31
Effective length of query: 367
Effective length of database: 367
Effective search space:   134689
Effective search space used:   134689
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 (21.6 bits)
S2: 50 (23.9 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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, 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