GapMind for catabolism of small carbon sources

 

Alignments for a candidate for put1 in Paenisporosarcina indica PN2

Align Proline dehydrogenase 1; PRODH 1; Proline oxidase 1; EC 1.5.5.2 (characterized)
to candidate WP_075618754.1 GY23_RS08375 proline dehydrogenase

Query= SwissProt::Q8RMG1
         (302 letters)



>NCBI__GCF_001939075.1:WP_075618754.1
          Length = 330

 Score =  285 bits (728), Expect = 1e-81
 Identities = 135/302 (44%), Positives = 203/302 (67%), Gaps = 2/302 (0%)

Query: 1   MLRHVFLFLSQNKTLTKFAKAYGTRLGARRFVAGDTIESAVKTVKRLNRSGLCATIDYLG 60
           +L+ VF+ LSQN+ L   AK YG ++GA+  VAG  +E  +K++K LN  G+ AT+D LG
Sbjct: 3   ILKDVFMSLSQNQLLNSAAKKYGLKMGAQTVVAGTNVEETIKSIKELNAQGISATVDNLG 62

Query: 61  EYAASEKEANQVAEECKKAIQAIAEHQLDSELSLKLTSIGLDLSEELALTHLRAILSVAK 120
           E+   ++EA +      + I+AI EH +D+ +SLK T +GLD+  +    +L+ I++ A 
Sbjct: 63  EFVFEKEEAIKAKNNILEVIEAINEHGVDAHISLKATQLGLDIDFDFCYENLKGIVAAAS 122

Query: 121 QYDVAVTIDMEDYSHYEQTLSIYRQCKQEFEKLGTVIQAYLYRAAEDIKKMRDLKPNLRL 180
           +YD+ + IDMEDY H + +  +  +  QE+  +GTVIQAY YRA +DI++ ++L+  LR+
Sbjct: 123 KYDMHINIDMEDYGHLQPSFDLMDKLLQEYSNVGTVIQAYFYRAQDDIEQYKNLR--LRI 180

Query: 181 VKGAYKESAAVAFPDKRGTDLHFQSLIKLQLLSGNYTAVATHDDDIIKFTKQLVAEHRIP 240
           VKGAYKESA  A+  K   D ++  LI+  LL+G ++++ATHD ++I   K+ V EH+IP
Sbjct: 181 VKGAYKESAEHAYQTKEEIDANYIKLIEYHLLNGKFSSIATHDHNVINHVKKFVEEHQIP 240

Query: 241 ASQFEFQMLYGIRPERQKELAKEGYRMRVYVPYGTDWFSYFMRRIAERPANAAFVLKGIL 300
             ++EFQMLYG R + Q +LAK+GY    YVP+G DW+ YFMRR+AERPAN   V+K + 
Sbjct: 241 KDKYEFQMLYGFRKDMQVDLAKQGYNFCTYVPFGDDWYGYFMRRLAERPANLNLVVKQVF 300

Query: 301 KK 302
            K
Sbjct: 301 NK 302


Lambda     K      H
   0.321    0.134    0.376 

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: 302
Length of database: 330
Length adjustment: 27
Effective length of query: 275
Effective length of database: 303
Effective search space:    83325
Effective search space used:    83325
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 (21.9 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