GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dddA in Dyella japonica UNC79MFTsu3.2

Align 3-hydroxypropionate dehydrogenase (EC 1.1.1.59) (characterized)
to candidate N515DRAFT_4337 N515DRAFT_4337 Choline dehydrogenase

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



>FitnessBrowser__Dyella79:N515DRAFT_4337
          Length = 533

 Score =  357 bits (915), Expect = e-103
 Identities = 222/554 (40%), Positives = 304/554 (54%), Gaps = 39/554 (7%)

Query: 36  FDYIVVGAGTAGCLLANRLSADPANRVLLIEAGGRDNYHWIHIPVGYLYCINNPR----- 90
           +DY++VG G+AGC+LANRLSA P  RVLL+EAG RD    IH+P G    + + R     
Sbjct: 3   YDYVIVGGGSAGCVLANRLSAQPGKRVLLLEAGPRDLNPLIHMPAGIAKLVGDHRGLARL 62

Query: 91  -----TDWRFRTEPDPGLNGRSLIYPRGKTLGGCSSINGMLYLRGQARDYDGWAELTGDD 145
                 +W +RTEP   L  R L +PRGKTLGG SSIN M Y+RG A DY+ WA+ TGD+
Sbjct: 63  YGSGRINWGYRTEPQAQLMNRRLWWPRGKTLGGSSSINAMCYIRGAAGDYEAWAQATGDE 122

Query: 146 AWRWDNCLPDFMRHEDHYRLDEGGDADPDHYKFHGHGGEWRIEKQRLKWQVLADFATAAV 205
            WRWD  L  F+R ED+ R      A P    +HG GG   +   R   ++   F  A  
Sbjct: 123 RWRWDAVLSWFLRGEDNAR-----GAGP----WHGAGGPLSVADLRFHSELSDAFVAAGA 173

Query: 206 EAGVPRTRDFNRGDNEGVDAFEVNQRSGWRWNASKAFLRGVEQRGNLTVWHSTQVLKLDF 265
            AG  R  DFN    +G   ++V QR G R +A+ A+LR   QR NL V     V ++  
Sbjct: 174 AAGFARNDDFNGARQDGFGLYQVTQRDGARCSAAVAYLRPALQRANLEVRTGALVQRVLI 233

Query: 266 ASGEGSEPRCCGVTVERAGKKVVTTARCEVVLSAGAIGSPQLLQLSGIGPTALLAEHAIP 325
             G     R  GV V   G+++      EV+L+AGA+ +PQLL LSGIGP   L EH +P
Sbjct: 234 EQG-----RAVGVQV--GGRRIEAG---EVILAAGAVNTPQLLMLSGIGPADHLREHGVP 283

Query: 326 VVADLPGVGENLQDHLQIRSIYKVKGAKTLNTMANSLIGKAKIGLEYILKRSGPMSMAPS 385
           V+ D P VG +LQDHL I S+       T + + N L     +   Y   R G  +   +
Sbjct: 284 VLLDQPHVGAHLQDHLDICSVVGTHSRATFDHL-NDL----AVAWRYARHRDGIGTSNAA 338

Query: 386 QLCIFTRS-SKEYEHPNLEYHVQPLSLEAFGQPLHDFPAITASVCNLNPTSRGTVRIKSG 444
           +   F RS     E  ++++H  P  L+  G         T   C L+P SRG +R++S 
Sbjct: 339 EAGGFVRSRHAPDERCDIQFHFIPAQLDDHGAHALPGRGYTVHACYLHPRSRGRLRLRSA 398

Query: 445 NPRQAPAISPNYLSTEE--DRQVAADSLRVTRHIASQPAFAKYDPEEFKPGVQYQSDEDL 502
           +P    AI  NYL   +  D ++  ++ R++R I +Q  F  +     +P  + ++D + 
Sbjct: 399 DPAVPIAIHANYLGDAQGHDLKLMIEAARLSREILAQAPFDAFRGAPVQPAGELRTDTEY 458

Query: 503 ARLAGDIGTTIFHPVGTAKMGRDDDPMAVVDSHLRVRGVTGLRVVDASIMPTITSGNTNS 562
           A        TI+HPVGT +MGR+ +  AVVDS LRV G+ GLRV DAS+MPT+ +GNTN+
Sbjct: 459 ADFIRRRAETIYHPVGTCRMGREHE--AVVDSELRVWGLPGLRVADASVMPTLVTGNTNA 516

Query: 563 PTLMIAEKAAGWIL 576
           PTLMIAE+AA  +L
Sbjct: 517 PTLMIAERAAALML 530


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: 967
Number of extensions: 49
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: 533
Length adjustment: 36
Effective length of query: 543
Effective length of database: 497
Effective search space:   269871
Effective search space used:   269871
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