Aligments for a candidate for dddA in Sphingomonas koreensis DSMZ 15582

GapMind for catabolism of small carbon sources

Aligments for a candidate for dddA in Sphingomonas koreensis DSMZ 15582

Align 3-hydroxypropionate dehydrogenase (EC 1.1.1.59) (characterized)
to candidate Ga0059261_2901 Ga0059261_2901 Choline dehydrogenase and related flavoproteins

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



>lcl|FitnessBrowser__Korea:Ga0059261_2901 Ga0059261_2901 Choline
           dehydrogenase and related flavoproteins
          Length = 562

 Score =  152 bits (385), Expect = 3e-41
 Identities = 178/600 (29%), Positives = 248/600 (41%), Gaps = 110/600 (18%)

Query: 36  FDYIVVGAGTAGCLLANRLSADPANRVLLIEAG-----GRDNYHWIHIPVGYLYCINNPR 90
           + +I++G G+AG +LA+RLS   AN+VLLIEAG     G +    +    G  Y   + R
Sbjct: 3   YSHIIIGGGSAGSVLASRLSERGANQVLLIEAGPDTPPGDEPAAILDSYPGSAYL--DAR 60

Query: 91  TDW---RFRTEPDPGLNGRSLIYPR----GKTLGGCSSINGMLYLRGQARDYDGWAELTG 143
             W   R    P   L   +++ PR     + LGG S+ING L  RG   D++ W    G
Sbjct: 61  FVWSNRRVTVAPTGNLQPGTMLPPRKYEQARVLGGGSAINGQLANRGLPWDFEDWVA-RG 119

Query: 144 DDAWRWDNCLPDFMRHEDHYRLDEGGDADPDHYKFHGHGGEWRIEK-QRLKWQVLAD-FA 201
              W WD+ LP F + E+    D            HG+ G   I +     W   A  F+
Sbjct: 120 AMGWGWDDVLPFFRKLENDLDFDG---------PLHGNTGPLPIRRIPEAFWPGQAKAFS 170

Query: 202 TAAVEAGVPRTRDFNRGDNEGVDAFEVNQRSGWRWNASKAFLR-GVEQRGNLTVWHSTQV 260
            A  EAG+P   D N    +G     ++     R  A+ A+L   V  R NL +  +T V
Sbjct: 171 AALTEAGLPFLADQNGEFGDGHYPLPISNIDNHRVTAAMAWLTLQVRSRSNLQIRTNTTV 230

Query: 261 LKLDFASGEGSEPRCCGVTVERAGKKVVTTARCEVVLSAGAIGSPQLLQLSGIGPTALLA 320
             L F        R  GV   RAG +V+      ++LSAGA+ +P+LL  SGIGP   LA
Sbjct: 231 EALLFDG-----LRAIGV---RAGGEVLLGKT--IILSAGALMTPELLLRSGIGPADDLA 280

Query: 321 EHAIPVVADLPGVGENLQDHLQIRSIYKVKGAKTLNTMANSLIGKAKIGLEYILKRSGPM 380
              + V  + PGVG  L DH  I     +  A  L      ++   +   +     +G M
Sbjct: 281 RVGVEVRLNAPGVGRGLTDHPSIAIASYLPSAARLRRQRRHILLGVRFSTDTNRFPAGDM 340

Query: 381 SMAPSQLCIFTRSSKEYEHPNLEYHVQPLSLEAFGQPLHDFPAITASVCNLNPTSRGTVR 440
           S       I T+++         +H       A G+ L       A   N   +  G + 
Sbjct: 341 SG-----LISTKAA---------WH-------AVGERL----GTLAFWINRPLSEDGRIH 375

Query: 441 IKSGNPRQAPAISPNYLSTEED--------RQVAADSLRVTRHIASQPAF-AKYDPEEFK 491
           + S +PRQA  +  N LS   D        R++AA  L      A+  AF A Y  +  +
Sbjct: 376 LTSADPRQAAQVDFNLLSDSRDVERLMRGFRRMAALHLSPLLGNAALDAFPASYSEKVRQ 435

Query: 492 PGVQYQSDEDLARLAG------------------------------DIGTTIF------- 514
            G     +  L RLA                               D    +F       
Sbjct: 436 IGTINLKNRILTRLAALFLDGPAPIRRAFIENLVMEGESIADLLSDDAKLEVFVRSAVAG 495

Query: 515 --HPVGTAKMGRDDDPMAVVDSHLRVRGVTGLRVVDASIMPTITSGNTNSPTLMIAEKAA 572
             H   + +MG  DDPMAV+    RV+G+ GLRV DAS  P I S NTN   LM+AEK A
Sbjct: 496 VWHASCSCRMGAADDPMAVLTPDGRVKGIEGLRVSDASAFPAIPSANTNLAVLMLAEKLA 555


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: 805
Number of extensions: 40
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 579
Length of database: 562
Length adjustment: 36
Effective length of query: 543
Effective length of database: 526
Effective search space:   285618
Effective search space used:   285618
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