GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dddA in Burkholderia phytofirmans PsJN

Align 3-hydroxypropionate dehydrogenase (EC 1.1.1.59) (characterized)
to candidate BPHYT_RS19495 BPHYT_RS19495 choline dehydrogenase

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



>FitnessBrowser__BFirm:BPHYT_RS19495
          Length = 570

 Score =  646 bits (1667), Expect = 0.0
 Identities = 328/556 (58%), Positives = 403/556 (72%), Gaps = 24/556 (4%)

Query: 30  TNNTHA-------FDYIVVGAGTAGCLLANRLSADPANRVLLIEAGGRDNYHWIHIPVGY 82
           T+ THA       FDYI+VGAGTAGC+LANRL+ DP  +VLL+EAGG+D+YHWIH+PVGY
Sbjct: 4   TDTTHATRRLEGEFDYIIVGAGTAGCVLANRLTQDPDVQVLLLEAGGKDDYHWIHVPVGY 63

Query: 83  LYCINNPRTDWRFRTEPDPGLNGRSLIYPRGKTLGGCSSINGMLYLRGQARDYDGWAELT 142
           LYCI NPRTDW ++T+ + GLNGR+L YPRG+ LGG SSINGM+Y+RGQ  DYD WA +T
Sbjct: 64  LYCIGNPRTDWLYKTQAEAGLNGRALSYPRGRVLGGSSSINGMIYMRGQREDYDEWARVT 123

Query: 143 GDDAWRWDNCLPDFMRHEDHYRLDEGGDADPDHYKFHGHGGEWRIEKQRLKWQVLADFAT 202
            D +W W++ LP F R EDH+     G ++      HG GG WR+EKQRLKW++L +F+ 
Sbjct: 124 NDASWSWNSVLPVFKRSEDHH----AGASES-----HGAGGPWRVEKQRLKWKILEEFSR 174

Query: 203 AAVEAGVPRTRDFNRGDNEGVDAFEVNQRSGWRWNASKAFLRGVEQRGNLTVWHSTQVLK 262
           AA E G+P T DFNRGDN GV  F+VNQ+ G RWNASKAFLR   +R NLTV       +
Sbjct: 175 AAQETGIPATDDFNRGDNTGVGYFDVNQKRGIRWNASKAFLRPALKRPNLTVITGAYTQR 234

Query: 263 LDFASGEGSEPRCCGVTVERAGKKVVTTARCEVVLSAGAIGSPQLLQLSGIGPTALLAEH 322
           + F   EG   RC GV         +  ARCEV+LS+GA+ SPQLL+LSGIG  A L   
Sbjct: 235 VVF---EGR--RCTGVEYRGDNTDYLAKARCEVILSSGAVNSPQLLELSGIGNGARLQNL 289

Query: 323 AIPVVADLPGVGENLQDHLQIRSIYKVKGAKTLNTMANSLIGKAKIGLEYILKRSGPMSM 382
            I VV DL GVGENLQDHLQ+R  YKV G +TLNT +    GK  IG++Y   +SGPMSM
Sbjct: 290 GIEVVDDLRGVGENLQDHLQLRMAYKVDGVRTLNTASAHWWGKLLIGMQYAFFQSGPMSM 349

Query: 383 APSQLCIFTRSS---KEYEHPNLEYHVQPLSLEAFGQPLHDFPAITASVCNLNPTSRGTV 439
           +PSQL  F +S    +    P+LEYHVQPLSL+ FG+PLH F A TASVC L PTSRG++
Sbjct: 350 SPSQLGAFAKSDPGDRSLTRPDLEYHVQPLSLDRFGEPLHRFNAFTASVCQLRPTSRGSI 409

Query: 440 RIKSGNPRQAPAISPNYLSTEEDRQVAADSLRVTRHIASQPAFAKYDPEEFKPGVQYQSD 499
            I+S +    P I+PNYLST+ DR VAA++LR+TR IA+ PA A+Y P+E  PG+QYQ++
Sbjct: 410 HIESADASAPPLIAPNYLSTDYDRHVAANALRLTRRIAAAPALARYRPQEILPGIQYQTE 469

Query: 500 EDLARLAGDIGTTIFHPVGTAKMGRDDDPMAVVDSHLRVRGVTGLRVVDASIMPTITSGN 559
           E+L + AG +GTTIFHPVGT +MG  DDP AVVD+ LRV GV GLRVVDAS+MPTITSGN
Sbjct: 470 EELQQAAGAVGTTIFHPVGTCRMGTTDDPGAVVDNRLRVIGVDGLRVVDASVMPTITSGN 529

Query: 560 TNSPTLMIAEKAAGWI 575
           TNSPTLMIAE+A+  I
Sbjct: 530 TNSPTLMIAERASDMI 545


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: 991
Number of extensions: 36
Number of successful extensions: 4
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: 570
Length adjustment: 36
Effective length of query: 543
Effective length of database: 534
Effective search space:   289962
Effective search space used:   289962
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