Aligments for a candidate for dddA in Caulobacter crescentus NA1000

GapMind for catabolism of small carbon sources

Aligments 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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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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

GapMind for catabolism of small carbon sources