GapMind for catabolism of small carbon sources

 

Aligments for a candidate for dddA in Pseudomonas putida KT2440

Align 3-hydroxypropionate dehydrogenase (EC 1.1.1.59) (characterized)
to candidate PP_1949 PP_1949 Oxidoreductase, GMC family

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



>lcl|FitnessBrowser__Putida:PP_1949 PP_1949 Oxidoreductase, GMC
           family
          Length = 550

 Score =  372 bits (954), Expect = e-107
 Identities = 229/548 (41%), Positives = 302/548 (55%), Gaps = 25/548 (4%)

Query: 36  FDYIVVGAGTAGCLLANRLSADPANRVLLIEAGGRDNYHWIHIPVGYLYCINNPRTDWRF 95
           +DYI++GAG+AGC+LANRLSA+P + VLL+EAG R    W  +P G    I    T+W +
Sbjct: 8   YDYIIIGAGSAGCVLANRLSANPEHSVLLLEAGSRPKGLWASMPAGVSRVILPGPTNWAY 67

Query: 96  RTEPDPGLNGRSLIYPRGKTLGGCSSINGMLYLRGQARDYDGWAELTGDDAWRWDNCLPD 155
           ++EPDP L GR +  PRGK LGG S+INGM YLRG   DYD W  L G   W WD+ LP 
Sbjct: 68  QSEPDPSLAGRRIYVPRGKALGGSSAINGMAYLRGHREDYDHWVSL-GCAGWGWDDVLPF 126

Query: 156 FMRHEDHYRLDEGGDADPDHYKFHGHGGEWRIEKQRLKWQVLADFATAAVEAGVPRTRDF 215
           + + E     +EG +A      F G  GE  +     K      F  + VEAG+PR  D 
Sbjct: 127 YKKFEHR---EEGDEA------FRGRDGELWVTDPVFKHPSSQAFIESCVEAGIPRLDDL 177

Query: 216 NRGDNEGVDAFEVNQRSGWRWNASKAFLRGVEQRGNLTVWHSTQVLKLDFASGEGSEPRC 275
           N    EG    +   + G R +A+ AFL+ V +R NL V     V K+   +      R 
Sbjct: 178 NAPSPEGTGFLQFTIKGGRRHSAATAFLQPVLKRPNLHVLTGALVQKIVIEA-----ERA 232

Query: 276 CGVTVERAGKKVVTTARCEVVLSAGAIGSPQLLQLSGIGPTALLAEHAIPVVADLPGVGE 335
            GV      + +   AR E++LSAGAI SP+LL LSG+GP   L  H IPV+ DLPGVGE
Sbjct: 233 TGVEYSLGNQSIFAAAR-EIILSAGAIDSPKLLMLSGVGPAQELTRHGIPVLRDLPGVGE 291

Query: 336 NLQDHLQIRSIYKVKGAKTLNTMANSLIGKAKIGLEYILKRSGPMSMAPSQLCIFTRSSK 395
           NL DH+ + S  +     +LN     L    + G+ Y+L+  G ++M  SQ     +   
Sbjct: 292 NLHDHVYVHSGIETDRVASLNKDLRGLRSVLQ-GMNYLLRGKGCLTMGASQAVALAQVLP 350

Query: 396 EYEHPNLEYHVQPLSLEAFGQPLHDF---PAITASVCNLNPTSRGTVRIKSGNPRQAPAI 452
               P+ + + +PLS     Q L +     A+T S C LNP SRG + +KS NP  APAI
Sbjct: 351 GARRPDTQINYRPLSWHFNKQGLVEIGKDNAVTISTCQLNPLSRGRLTLKSSNPIDAPAI 410

Query: 453 SPNYLSTEEDRQVAADSLRVTRHIASQPAFAKYDPEEFKPGVQYQSDEDLARLAGDIG-T 511
            PNY   E D   A  ++R  R I+     AK+      P     SD ++A      G +
Sbjct: 411 YPNYFGNERDMVAAIAAVRKVREISCVGPLAKHIVNISPP--DSMSDGEIADYIRQEGAS 468

Query: 512 TIFHPVGTAKMGRDDDPMAVVDSHLRVRGVTGLRVVDASIMPTITSGNTNSPTLMIAEKA 571
           ++ H VG+ KMG D   MAVVD  L+VRG+ GLRVVDASIMPTITSGNTN+PT+MI EK 
Sbjct: 469 SMMHWVGSCKMGIDS--MAVVDERLKVRGLQGLRVVDASIMPTITSGNTNAPTIMIGEKG 526

Query: 572 AGWILKSQ 579
           A  IL+ +
Sbjct: 527 AAMILEDR 534


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: 883
Number of extensions: 45
Number of successful extensions: 7
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: 550
Length adjustment: 36
Effective length of query: 543
Effective length of database: 514
Effective search space:   279102
Effective search space used:   279102
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 preprint 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