GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dddA in Pseudomonas stutzeri RCH2

Align 3-hydroxypropionate dehydrogenase (EC 1.1.1.59) (characterized)
to candidate GFF2583 Psest_2633 choline dehydrogenase

Query= metacyc::MONOMER-15202
         (579 letters)



>FitnessBrowser__psRCH2:GFF2583
          Length = 557

 Score =  334 bits (857), Expect = 5e-96
 Identities = 214/542 (39%), Positives = 297/542 (54%), Gaps = 22/542 (4%)

Query: 36  FDYIVVGAGTAGCLLANRLSADPANRVLLIEAGGRDNY--HWIHIPVGYLYCINNPRTDW 93
           +DYI++GAG+AG +LA RL+ D    VLL+EAGG D        +P    Y +   R +W
Sbjct: 3   YDYIIIGAGSAGNVLAARLTEDADVSVLLLEAGGPDYRLDFRTQMPAALAYPLQGTRYNW 62

Query: 94  RFRTEPDPGLNGRSLIYPRGKTLGGCSSINGMLYLRGQARDYDGWAELTGDDAWRWDNCL 153
            ++T+P+P +N R +   RGK LGG S INGM Y+RG A DYD WA+  G + W + +CL
Sbjct: 63  AYKTDPEPHMNNRRMDCGRGKGLGGSSLINGMCYIRGNALDYDNWAKAPGLEDWTYLDCL 122

Query: 154 PDFMRHEDHYRLDEGGDADPDHYKFHGHGGEWRIEKQRLKWQVLAD-FATAAVEAGVPRT 212
           P       ++R  E  D  P+ Y  HG  G   +   R    VL      A V+AG PRT
Sbjct: 123 P-------YFRKAESRDIGPNDY--HGGVGPVSVTTPRADNNVLFQAMVEAGVQAGYPRT 173

Query: 213 RDFNRGDNEGVDAFEVNQR-SGWRWNASKAFLRGVEQRGNLTVWHSTQVLKLDFASGEGS 271
            D N    EG    +      G R + ++ +L    +R NLT+       ++ F   EG 
Sbjct: 174 DDLNGYQQEGFGPMDRTVTPQGRRASTARGYLDQARERPNLTIETHAVTDRVLF---EGK 230

Query: 272 EPRCCGVTVERAGKK-VVTTARCEVVLSAGAIGSPQLLQLSGIGPTALLAEHAIPVVADL 330
             R  GV   R  K   +  AR EV+L  GAI SPQ+LQ SG+GP ALL    +  V +L
Sbjct: 231 --RAVGVRYLRDRKDPYIARARREVLLCGGAIASPQILQRSGVGPGALLRRVGVKPVHEL 288

Query: 331 PGVGENLQDHLQIRSIYKVKGAKTLNTMANSLIGKAKIGLEYILKRSGPMSMAPSQLCIF 390
           PGVG+NLQDHL++   Y+ K   +L   A     +  IG E++   SG  +    +   F
Sbjct: 289 PGVGQNLQDHLEMYLQYECKQPVSLYP-ALKWWNQPAIGAEWLFLGSGIGASNQFEAGGF 347

Query: 391 TRSSKEYEHPNLEYHVQPLSLEAFGQPLHDFPAITASVCNLNPTSRGTVRIKSGNPRQAP 450
            RSS E+E PN+++H  P+++   G   HD  +  A V ++   SRG + I+S +P + P
Sbjct: 348 IRSSDEFEWPNIQFHFLPVAVSYNGSNAHDGHSFQAHVGSMRSPSRGRIEIRSTDPAEDP 407

Query: 451 AISPNYLSTEEDRQVAADSLRVTRHIASQPAFAKYDPEEFKPGVQYQSDEDLARLAGDIG 510
           +I  NY++ E+D +   D +R+TR I +QPA   Y   E  PG++ QSD +L     +  
Sbjct: 408 SILFNYMAHEQDWREFRDGIRLTREIMNQPALDPYRGRELSPGIEAQSDAELDAFVREHA 467

Query: 511 TTIFHPVGTAKMGRDDDPMAVVDSHLRVRGVTGLRVVDASIMPTITSGNTNSPTLMIAEK 570
            T +HP  + KMG DD  MAVVD   RV G+ GLRVVDASIMP I +GN N+ T+MIAEK
Sbjct: 468 ETAYHPSCSCKMGTDD--MAVVDGQGRVHGMEGLRVVDASIMPQIITGNLNATTIMIAEK 525

Query: 571 AA 572
            A
Sbjct: 526 IA 527


Lambda     K      H
   0.318    0.135    0.418 

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: 981
Number of extensions: 60
Number of successful extensions: 6
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: 579
Length of database: 557
Length adjustment: 36
Effective length of query: 543
Effective length of database: 521
Effective search space:   282903
Effective search space used:   282903
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