GapMind for catabolism of small carbon sources

 

Alignments for a candidate for put1 in Phaeobacter inhibens BS107

Align proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate GFF3260 PGA1_c33110 sarcosine dehydrogenase

Query= BRENDA::Q8U022
         (378 letters)



>FitnessBrowser__Phaeo:GFF3260
          Length = 816

 Score =  150 bits (380), Expect = 9e-41
 Identities = 116/370 (31%), Positives = 176/370 (47%), Gaps = 29/370 (7%)

Query: 4   IIGGGIIGVATAYELAKLG-EEVVVFEKRYFGSGSTFRCASGIRAQFTDEANI-KLMKYS 61
           IIGGG+IG + AY L KLG ++VV+ E++   SG+T+  A+G+ AQ    AN+ KL KYS
Sbjct: 12  IIGGGVIGCSVAYHLTKLGWKDVVLLERKQLTSGTTWH-AAGLIAQLRATANMTKLAKYS 70

Query: 62  IERWKTLSEELGHNIMFQQTGYLFLATTEEEVEAFKKNIKLQNKFGVPTRLITPEEAKEI 121
            E +  L EE G    F++ G + +A TEE  E   +   +   FGV    I+PEE K  
Sbjct: 71  QELYGALEEETGVATGFKRCGSITVALTEERKEEIFRQAAMARAFGVEVEEISPEEVKTR 130

Query: 122 VPPLNADAFLAGAWNPEDGKASPFHTLYAYKKAGERLGVKFYEYTKVVGIEKDGSK---- 177
              LN     AG W P+DG+  P +   A  K   + G    E  KV GI K+G +    
Sbjct: 131 YEHLNVGDVTAGVWLPKDGQGDPANIALALAKGARQRGALVKERIKVTGISKEGRRATGV 190

Query: 178 -WKI--KTTRGEFKVDIIINATNAWAREINKMIGKDIIPVTPYKHQLVKTEPIERGQIEP 234
            W      ++G  + D+++N    W  E+ +M G + +P+   +H  + TE I      P
Sbjct: 191 DWASDDSQSQGHIEADMVVNCAGMWGHEVGRMAGVN-VPLHACEHFYIVTEGITGLTQMP 249

Query: 235 LVCPPAWNDSYVIQDGEDGGVICGTALEYESSP---DDVTPTYEF---------VKEVLK 282
           ++  P     Y     ED G I   A E  + P   + +  T+EF          + +L+
Sbjct: 250 VLRVPDECAYY----KEDAGKILLGAFEPNAKPWAMNGIPDTFEFDQLPEDFDHFEPILE 305

Query: 283 WAVKIIPALKHVHVVRQWAGHYAKTPDKNPAIGMIEE--NFYVAVGFSGHGFMMAPAVAQ 340
            A   +P L    +   + G  + TPD    +G+  E  N +VA GF+  G   A     
Sbjct: 306 AACNRMPMLAEAGIHTFFNGPESFTPDDAYHLGLAPEMDNVWVAAGFNSIGIQSAGGAGM 365

Query: 341 ALAEKIVEGK 350
           ALA+ + +G+
Sbjct: 366 ALAQWMEDGQ 375


Lambda     K      H
   0.318    0.137    0.420 

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: 751
Number of extensions: 42
Number of successful extensions: 4
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: 378
Length of database: 816
Length adjustment: 36
Effective length of query: 342
Effective length of database: 780
Effective search space:   266760
Effective search space used:   266760
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 (21.7 bits)
S2: 53 (25.0 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