GapMind for catabolism of small carbon sources

 

Alignments for a candidate for put1 in Planococcus halocryophilus Or1

Align Proline dehydrogenase 2; PRODH 2; Proline oxidase 2; EC 1.5.5.2 (characterized)
to candidate WP_008498617.1 B481_RS13765 proline dehydrogenase family protein

Query= SwissProt::P94390
         (303 letters)



>NCBI__GCF_000342445.1:WP_008498617.1
          Length = 302

 Score =  297 bits (760), Expect = 2e-85
 Identities = 143/302 (47%), Positives = 208/302 (68%), Gaps = 2/302 (0%)

Query: 2   ITRDFFLFLSKSGFLNKMARNWGSRVAAGKIIGGNDFNSSIPTIRQLNSQGLSVTVDHLG 61
           +T++FF+ LSK+  LN  A+ WG ++ AGK++ G D  S + ++++LN+ G+S T+D LG
Sbjct: 3   VTKNFFIALSKNQPLNSAAKKWGLKLGAGKVVAGTDIASMMQSVKELNANGISATIDSLG 62

Query: 62  EFVNSAEVARERTEECIQTIATIADQELNSHVSLKMTSLGLDIDMDLVYENMTKILQTAE 121
           EFV++ E A +  E  I+T+ +I    +N+H+S+K+T +GLD+D D   +N+ +IL  A 
Sbjct: 63  EFVHTKEEATKAKEAIIKTLESIQIYGVNAHMSVKLTQIGLDVDFDFCLKNIQEILAEAS 122

Query: 122 KHKIMVTIDMEDEVRCQKTLDIFKDFRKKYEHVSTVLQAYLYRTEKDIDDLDSLNPFLRL 181
           ++ I + +DMED    Q+TLDI +  R +YE+V TV+QAYLYR+EKD++ L  +   LRL
Sbjct: 123 RYDIFINLDMEDYDHLQQTLDILEALRAEYENVGTVIQAYLYRSEKDLETLKDVR--LRL 180

Query: 182 VKGAYKESEKVAFPEKSDVDENYKKIIRKQLLNGHYTAIATHDDKMIDFTKQLAKEHGIA 241
           VKGAYKES +V+F EK +VDENY K+I+  L +  +T+IATHD  +I+  K   KE  I 
Sbjct: 181 VKGAYKESSEVSFQEKHEVDENYLKLIKIHLQSPGFTSIATHDHHIIEKVKAFVKEENIP 240

Query: 242 NDKFEFQMLYGMRSQTQLSLVKEGYNMRVYLPYGEDWYGYFMRRLAERPSNIAFAFKGMT 301
            ++FEFQMLYG RS+ Q  L KEGY    Y+P+G+DWY Y+MRRLAERP NI    + M 
Sbjct: 241 LNRFEFQMLYGFRSEMQKDLAKEGYAFTTYVPFGQDWYAYYMRRLAERPQNINLMLRSMI 300

Query: 302 KK 303
            K
Sbjct: 301 SK 302


Lambda     K      H
   0.320    0.135    0.383 

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: 270
Number of extensions: 9
Number of successful extensions: 2
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: 303
Length of database: 302
Length adjustment: 27
Effective length of query: 276
Effective length of database: 275
Effective search space:    75900
Effective search space used:    75900
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 (21.8 bits)
S2: 48 (23.1 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