GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Putida:PP_1949
          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:

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