GapMind for catabolism of small carbon sources

 

Alignments for a candidate for put1 in Mariniradius saccharolyticus AK6

Align Proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate WP_008623424.1 C943_RS00910 proline dehydrogenase family protein

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



>NCBI__GCF_000330725.2:WP_008623424.1
          Length = 396

 Score =  550 bits (1417), Expect = e-161
 Identities = 271/395 (68%), Positives = 326/395 (82%)

Query: 1   MNTKPNISFENTEIAFASRTDAELRKMYLFFAVMDKNWAVKIGTNLSAVAFKLKLPVKGI 60
           M  KPNISFEN E+AFAS++DAEL+KMYL FA ++ N AV +GT L+  +F L LP+KG+
Sbjct: 1   MQVKPNISFENLEVAFASKSDAELKKMYLIFATINNNLAVSVGTKLANWSFALGLPIKGL 60

Query: 61  MKKTIFGHFCGGESVEDCSKSIQELQEFGIGTILDYSVEGTGTEKSYDFTRDEILRTIER 120
           MKKT+FGHFCGGE++EDC KS+  L ++ I TILDYSVEG G E+S+D T++EIL+TIER
Sbjct: 61  MKKTMFGHFCGGENIEDCQKSVDVLAKYHIHTILDYSVEGKGDEESFDATKNEILKTIER 120

Query: 121 SAGASEIPFSVFKVTGLGSYKIMTKVQAGQKLSAKEQEAFERLKDRVDTLCKAAYENDVR 180
           SAG   +PF+VFKVTGLG + IMTK+QAGQ+LS  E+E+FE+LK RVD LC AA+  + +
Sbjct: 121 SAGDENMPFAVFKVTGLGDFGIMTKIQAGQQLSNGEKESFEKLKARVDELCAAAHAANTK 180

Query: 181 IMIDGEESWFQDVIDDMAYEAMEKYNKEKAIVYNTFQMYRKDMLGLLKKAHEEAELKGYH 240
           I+ID EESWFQ+VID MAYEAMEKYN+E  IVYNTFQMYR DMLG LKKAH+ A  KGY 
Sbjct: 181 ILIDAEESWFQEVIDKMAYEAMEKYNRESCIVYNTFQMYRHDMLGRLKKAHQIALEKGYW 240

Query: 241 VGAKLVRGAYMEKERDRAEDRGYPSPIQDTKEDTDNAYNDALKFSMEHKDRIYLVSGSHN 300
            GAKLVRGAYMEKERDRA + GYPSPIQ TKE +D  YN AL++ MEH   + LVSGSHN
Sbjct: 241 FGAKLVRGAYMEKERDRAAEMGYPSPIQPTKEASDRDYNAALEYCMEHIATMGLVSGSHN 300

Query: 301 ELSNIILTELMNLHGVAANDKRVYFSQLYGMSDNISYNLAFAGYNVAKYVPYGPVESVMP 360
           E SNI+LT+L++ +G++A+D RVYF+QLYGMSDNISYNLA AGYNV KYVPYGPVE VMP
Sbjct: 301 EQSNILLTQLLSKYGISASDDRVYFAQLYGMSDNISYNLAKAGYNVVKYVPYGPVEKVMP 360

Query: 361 YLYRRASENTSVAGQSSREFELIKNEMARRASLKK 395
           YL RRA ENTSVAGQSSREF+L+K E+ARR  LK+
Sbjct: 361 YLSRRAEENTSVAGQSSREFDLVKREIARRKKLKR 395


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: 559
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: 396
Length adjustment: 31
Effective length of query: 367
Effective length of database: 365
Effective search space:   133955
Effective search space used:   133955
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 24 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