GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dddA in Paraburkholderia bryophila 376MFSha3.1

Align 3-hydroxypropionate dehydrogenase (EC 1.1.1.59) (characterized)
to candidate H281DRAFT_00975 H281DRAFT_00975 choline dehydrogenase

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



>FitnessBrowser__Burk376:H281DRAFT_00975
          Length = 553

 Score =  365 bits (938), Expect = e-105
 Identities = 221/549 (40%), Positives = 308/549 (56%), Gaps = 24/549 (4%)

Query: 36  FDYIVVGAGTAGCLLANRLSADPANRVLLIEAGGRDNYHWIHIPVGYLYCINNPRTDWRF 95
           +DYI+VGAG+AGC+LANRLSA     VLL+EAGG+D+  W  +PVG+     N   +W +
Sbjct: 3   YDYIIVGAGSAGCILANRLSASGEYSVLLLEAGGKDSSFWFKVPVGFTKTYYNETYNWMY 62

Query: 96  RTEPDPGLNGRSLIYPRGKTLGGCSSINGMLYLRGQARDYDGWAELTGDDAWRWDNCLPD 155
            +EP+  L+ R +  PRGK  GG  SIN M+Y+RGQ  D+D WA   G+  W + + LP 
Sbjct: 63  YSEPEKELDNRPIYCPRGKVQGGSGSINAMIYVRGQPHDFDDWA-AAGNPGWAFRDVLPY 121

Query: 156 FMRHEDHYRLDEGGDADPDHYKFHGHGGEWRIEKQR-LKWQVLADFATAAVEAGVPRTRD 214
           F + E H      GD +     +HG  G  RI   +     +   F     +AG  R+ D
Sbjct: 122 FRKLESH----PLGDTE-----YHGADGPIRISPMKDAVHPICHVFLKGCDQAGYRRSDD 172

Query: 215 FNRGDNEGVDAFEVNQRSGWRWNASKAFLRGVEQRGNLTVWHSTQVLKLDFASGEGSEPR 274
           FN    EG   ++VN R+G R ++S  +L     R NLTV H+    ++ F   EG   R
Sbjct: 173 FNGAQFEGAGIYDVNTRNGQRSSSSFEYLHPALARKNLTVEHNVLANRVLF---EGKH-R 228

Query: 275 CCGVTVERAGKKVVTTARCEVVLSAGAIGSPQLLQLSGIGPTALLAEHAIPVVADLPGVG 334
             GV+V + G      A+ EV+L+AGA+ SP+LLQLSG+G +ALLA+H I  + +LP VG
Sbjct: 229 AIGVSVTQNGVARRFMAKREVILAAGAVDSPKLLQLSGLGDSALLAKHGITTIKELPAVG 288

Query: 335 ENLQDHLQIRSIYKVKGAKTLNTMANSLIGKAKIGLEYILKRSGPMSMAPSQLCIFTRSS 394
           +NLQDHL + S Y     KTLN     LIGK K+GL+Y+L R GP++M+ +Q   F R S
Sbjct: 289 QNLQDHLCV-SFYYRANVKTLNDELRPLIGKLKLGLQYLLTRKGPLAMSVNQSGGFFRGS 347

Query: 395 KEYEHPNLEYHVQPLSL------EAFGQPLHDFPAITASVCNLNPTSRGTVRIKSGNPRQ 448
           +    PNL+ +  PLS       +A  +P   +     +     PTSRG++ I S     
Sbjct: 348 EREAQPNLQLYFNPLSYRIPKSNKASLEP-EPYSGFLLAFNPCRPTSRGSIEIASNRAED 406

Query: 449 APAISPNYLSTEEDRQVAADSLRVTRHIASQPAFAKYDPEEFKPGVQYQSDEDLARLAGD 508
           A  I  N L+T++D         + R + + PA  +   EE  PG Q  S E   +   +
Sbjct: 407 AAKIRLNALTTQKDIDEVIQGCELVRKVMASPALKEITVEEISPGPQVASRESFLQYFRE 466

Query: 509 IGTTIFHPVGTAKMGRDDDPMAVVDSHLRVRGVTGLRVVDASIMPTITSGNTNSPTLMIA 568
              +I+H  G+  MG +D   +VVD+ LRV GV GLRVVDAS+ P ITSGN N+PT+M+A
Sbjct: 467 QSGSIYHLCGSCAMG-NDPRTSVVDARLRVHGVAGLRVVDASVFPNITSGNINAPTMMVA 525

Query: 569 EKAAGWILK 577
           EK A  IL+
Sbjct: 526 EKGADMILE 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: 847
Number of extensions: 37
Number of successful extensions: 6
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: 553
Length adjustment: 36
Effective length of query: 543
Effective length of database: 517
Effective search space:   280731
Effective search space used:   280731
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