GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__psRCH2:GFF2583 Psest_2633 choline dehydrogenase
          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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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