GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dddA in Caulobacter crescentus NA1000

Align 3-hydroxypropionate dehydrogenase (EC 1.1.1.59) (characterized)
to candidate CCNA_00994 CCNA_00994 oxidoreductase, GMC family

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



>FitnessBrowser__Caulo:CCNA_00994
          Length = 555

 Score =  419 bits (1076), Expect = e-121
 Identities = 241/557 (43%), Positives = 334/557 (59%), Gaps = 35/557 (6%)

Query: 37  DYIVVGAGTAGCLLANRLSADPANRVLLIEAGGRD----------NYHWIHIPVGYLYCI 86
           DY++VGAG+AGC+LA RLS +   +V+L+EAGG D          +   IHIPVGY   +
Sbjct: 8   DYVIVGAGSAGCVLAARLSENGRYKVVLLEAGGDDRPTKNLSQFASNMMIHIPVGYSSTL 67

Query: 87  NNPRTDWRFRTEPDPGLNGRSLIYPRGKTLGGCSSINGMLYLRGQARDYDGWAELTGDDA 146
            +P+ +W F TEPDPG  GRS ++PRGK LGG SSIN MLY+RGQA DYDGW +L G + 
Sbjct: 68  KDPKVNWLFTTEPDPGTGGRSHVWPRGKVLGGSSSINAMLYVRGQAADYDGWRQL-GCEG 126

Query: 147 WRWDNCLPDFMRHEDHYRLDEGGDADPDHYKFHGHGGEWRIEKQRLKWQVLADFATAAVE 206
           W WD+ LP F + ++     E G  D      H  GG   +   R    +      A  +
Sbjct: 127 WAWDDVLPYFRKAQN----QERGACD-----LHATGGPLNVADMRDAHPISEALIEACDQ 177

Query: 207 AGVPRTRDFNRGDNEGVDAFEVNQRSGWRWNASKAFLRGVEQRGNLTVWHSTQVLKLDFA 266
           AG+PR  D N  D EG   ++V Q++G R +++ A+L    +R NL V  +    ++ F 
Sbjct: 178 AGIPRYPDLNGADQEGATWYQVTQKNGARCSSAVAYLHPAMKRPNLRVETNALAGRVLF- 236

Query: 267 SGEGSEPRCCGVTVERAGKKVVTTARCEVVLSAGAIGSPQLLQLSGIGPTALLAEHAIPV 326
             EG   R  GV   + G++    AR EV+L+ GAI SPQLLQLSG+G   LL EH I V
Sbjct: 237 --EGK--RAVGVEFMQNGERRAAMARGEVILAGGAINSPQLLQLSGVGAGGLLREHGIEV 292

Query: 327 VADLPGVGENLQDHLQIRSIYKVKGAKTLNTMANSLIGK-AKIGLEYILKRSGPMSMAPS 385
           VADLPGVGENLQDH  + + Y++K   T++    S  G+ A   ++Y+L R G ++++ +
Sbjct: 293 VADLPGVGENLQDHYIVAARYRLKSG-TVSVNEQSKGGRLAAEAMKYLLFRKGLLTLSAA 351

Query: 386 QLCIFTRSSKEYEHPNLEYHVQPLSLE---AFGQ---PLHDFPAITASVCNLNPTSRGTV 439
            +  F +S  +   P++++H+ P +++    F +    L   P +T + C L P SRG +
Sbjct: 352 HVAAFCKSRPDLAGPDIQFHILPATMDLDKLFNEQKMELEGAPGMTIAPCQLRPESRGYI 411

Query: 440 RIKSGNPRQAPAISPNYLSTEEDRQVAADSLRVTRHIASQPAFAKYDPEEFKPGVQYQSD 499
           RIKS +P   PAI  NYL+   D++V    L+  R I  QPA A+Y   E  PG++ Q+D
Sbjct: 412 RIKSADPSVYPAIFANYLADPLDQEVIVAGLKWARKIGQQPAIAQYVESEMNPGLEVQTD 471

Query: 500 EDLARLAGDIGTTIFHPVGTAKMGRDDDPMAVVDSHLRVRGVTGLRVVDASIMPTITSGN 559
           E L   A   G+T++HPVG+ +MG    PMAVVD+ LRVRGV GLRVVDASIMP + SGN
Sbjct: 472 EQLLDFARQTGSTLYHPVGSCQMG--TGPMAVVDAQLRVRGVEGLRVVDASIMPRLISGN 529

Query: 560 TNSPTLMIAEKAAGWIL 576
           TN+P++MI EK A  IL
Sbjct: 530 TNAPSIMIGEKGADMIL 546


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: 921
Number of extensions: 39
Number of successful extensions: 8
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: 555
Length adjustment: 36
Effective length of query: 543
Effective length of database: 519
Effective search space:   281817
Effective search space used:   281817
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