GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dpkA in Pseudomonas fluorescens FW300-N1B4

Align Delta(1)-pyrroline-2-carboxylate/Delta(1)-piperideine-2-carboxylate reductase; Pyr2C/Pip2C reductase; N-methyl-L-amino acid dehydrogenase; EC 1.5.1.21; EC 1.4.1.17 (characterized)
to candidate Pf1N1B4_4705 Delta 1-piperideine-2-carboxylate reductase (EC 1.5.1.21) / Delta 1-pyrroline-2-carboxylate reductase (EC 1.5.1.1)

Query= SwissProt::Q4U331
         (343 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4705
          Length = 280

 Score =  392 bits (1006), Expect = e-114
 Identities = 201/276 (72%), Positives = 227/276 (82%), Gaps = 8/276 (2%)

Query: 1   MSASHADQPT---QTVSYPQLIDLLRRIFVVHGTSPEVADVLAENCASAQRDGSHSHGIF 57
           MSA H    T   Q +S+  L  LL +IF+ HGTS +VA  LA NCA A+RDG+HSHG+F
Sbjct: 1   MSAPHDPVSTAVSQNLSFEALTALLEQIFLRHGTSADVAKTLALNCAGAERDGAHSHGVF 60

Query: 58  RIPGYLSSLASGWVDGKAVPVVEDVGAAFVRVDACNGFAQPALAAARSLLIDKARSAGVA 117
           RIPGY+S+L SGWV+G+AVPVVEDV + FVRVDA NGFAQPALAAARSLL++KARSAG+A
Sbjct: 61  RIPGYVSTLQSGWVNGQAVPVVEDVASGFVRVDAGNGFAQPALAAARSLLVEKARSAGIA 120

Query: 118 ILAIRGSHHFAALWPDVEPFAEQGLVALSMVNSMTCVVPHGARQPLFGTNPIAFGAPRAG 177
           +LAIR SHHFAALWPDVEPFA++GLVALS+VNSMTCVVPHGA +PLFGTNPIAF APRA 
Sbjct: 121 VLAIRNSHHFAALWPDVEPFADEGLVALSVVNSMTCVVPHGADRPLFGTNPIAFAAPRAN 180

Query: 178 GEPIVFDLATSAIAHGDVQIAAREGRLLPAGMGVDRDGLPTQEPRAILDGGALLPFGGHK 237
           G PIVFDLATSAIAHGDVQIAAR+G  LPAGMGVD  G PTQ+P+A+L+GGALLPFGGHK
Sbjct: 181 GAPIVFDLATSAIAHGDVQIAARKGERLPAGMGVDSLGQPTQDPKAVLEGGALLPFGGHK 240

Query: 238 GSALSMMVELLAAGLTGGNF-----SFEFDWSKHPG 268
           GSALSMMVELLAA LTG  F            KHPG
Sbjct: 241 GSALSMMVELLAAALTGAIFLSSSTGRTIRGRKHPG 276


Lambda     K      H
   0.320    0.137    0.412 

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: 410
Number of extensions: 15
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: 343
Length of database: 280
Length adjustment: 27
Effective length of query: 316
Effective length of database: 253
Effective search space:    79948
Effective search space used:    79948
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)

Align Delta(1)-pyrroline-2-carboxylate/Delta(1)-piperideine-2-carboxylate reductase; Pyr2C/Pip2C reductase; N-methyl-L-amino acid dehydrogenase; EC 1.5.1.21; EC 1.4.1.17 (characterized)
to candidate Pf1N1B4_4706 Delta 1-piperideine-2-carboxylate reductase (EC 1.5.1.21) / Delta 1-pyrroline-2-carboxylate reductase (EC 1.5.1.1)

Query= SwissProt::Q4U331
         (343 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4706
          Length = 64

 Score = 81.6 bits (200), Expect = 4e-21
 Identities = 39/63 (61%), Positives = 50/63 (79%)

Query: 280 VIDPDKGAGQHFAQRSEELVRQLHGVGQERLPGDRRYLERARSMAHGIVIAQADLERLQE 339
           VIDP K AGQ+FA+RS+ELVRQ+HGVG +RLPGDRR+ +RA++   GIV+    L  L+E
Sbjct: 1   VIDPSKSAGQNFAERSQELVRQMHGVGLKRLPGDRRHRQRAKAGVEGIVLDAQTLANLRE 60

Query: 340 LAG 342
           LAG
Sbjct: 61  LAG 63


Lambda     K      H
   0.320    0.137    0.412 

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: 86
Number of extensions: 3
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: 343
Length of database: 64
Length adjustment: 16
Effective length of query: 327
Effective length of database: 48
Effective search space:    15696
Effective search space used:    15696
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: 42 (20.8 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