GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dddA in Caulobacter crescentus NA1000

Align 3-hydroxypropionate dehydrogenase (EC 1.1.1.59) (characterized)
to candidate CCNA_02725 CCNA_02725 choline dehydrogenase

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



>FitnessBrowser__Caulo:CCNA_02725
          Length = 555

 Score =  379 bits (974), Expect = e-109
 Identities = 225/543 (41%), Positives = 304/543 (55%), Gaps = 19/543 (3%)

Query: 36  FDYIVVGAGTAGCLLANRLSADPANRVLLIEAGGRDNYHWIHIPVGYLYCINNP-RTDWR 94
           FDYIV+GAG+AGC+LA RL+ DP  +VLL+EAGG++    + +P G    I +    +W 
Sbjct: 6   FDYIVIGAGSAGCVLAARLTEDPNIKVLLLEAGGKNKSILVKMPAGVGQLIKDKGEQNWG 65

Query: 95  FRTEPDPGLNGRSLIYPRGKTLGGCSSINGMLYLRGQARDYDGWAELTGDDAWRWDNCLP 154
           F TE +P L+ R L +PRGK LGG S+INGM+Y+RG ARDYD W ++ G   W +   LP
Sbjct: 66  FWTEAEPHLDNRKLWWPRGKGLGGSSAINGMIYIRGHARDYDQWRQM-GLTGWSYSEVLP 124

Query: 155 DFMRHEDHYRLDEGGDADPDHYKFHGHGGEWRIEKQRLKWQVLADFATAAVEAGVPRTRD 214
            F R E H+    GGDA      +HG  G   + K        +    A  +AG   T+D
Sbjct: 125 YFKRSETHHA---GGDA------YHGGSGPLHVSKGESDSPFYSTLVEAGRQAGHKTTKD 175

Query: 215 FNRGDNEGVDAFEVNQRSGWRWNASKAFLRGVEQRGNLTVWHS--TQVLKLDFASGEGSE 272
           FN    EG   +++  R G RW+A+ A+L     R NLT      T  + LD     G E
Sbjct: 176 FNGYQQEGFGPYDLTIRDGQRWSAAMAYLNQALSRPNLTCVTEACTTRIILDKRRAVGVE 235

Query: 273 PRCCGVTVERAGKKVVTTARCEVVLSAGAIGSPQLLQLSGIGPTALLAEHAIPVVADLPG 332
                  V ++ +K V  A  EV+LSAGA+ SPQ+LQLSGIG    LA H I V  +  G
Sbjct: 236 -----YVVGKSREKQVAYADAEVLLSAGAVQSPQILQLSGIGAAEDLAPHGIAVAHESKG 290

Query: 333 VGENLQDHLQIRSIYKVKGAKTLNTMANSLIGKAKIGLEYILKRSGPMSMAPSQLCIFTR 392
           VG NLQDHL +   +  K  KT  + AN  + K  +G+ Y+    G       +   F +
Sbjct: 291 VGANLQDHLDVCVSWTAKNLKTAYS-ANKGLNKLGVGMNYMFFGKGLGRQQFLESGAFLK 349

Query: 393 SSKEYEHPNLEYHVQPLSLEAFGQPLHDFPAITASVCNLNPTSRGTVRIKSGNPRQAPAI 452
           S  + + P+L+ H     ++  G+ + +    T  VC L P SRG V ++S +P   P I
Sbjct: 350 SRPDLDRPDLQIHGVLAIMQDHGKVVVEKDGFTLHVCQLRPESRGKVGLRSADPFDDPTI 409

Query: 453 SPNYLSTEEDRQVAADSLRVTRHIASQPAFAKYDPEEFKPGVQYQSDEDLARLAGDIGTT 512
             NYL+TEEDR+   + +R+ R   +Q AF  Y   E+ PG   +SD DL         T
Sbjct: 410 LGNYLATEEDRRAIREGVRIARETVAQAAFDPYRDAEYAPGADVKSDADLDAWIRSKAET 469

Query: 513 IFHPVGTAKMGRDDDPMAVVDSHLRVRGVTGLRVVDASIMPTITSGNTNSPTLMIAEKAA 572
           I+HPVGT +MG   DPMAVVD  LRV+GV GLRV+DAS+MPT+  GNTN+PT+MIAE+AA
Sbjct: 470 IYHPVGTCRMGVAGDPMAVVDDQLRVQGVQGLRVIDASVMPTLIGGNTNAPTIMIAERAA 529

Query: 573 GWI 575
             I
Sbjct: 530 DLI 532


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: 878
Number of extensions: 42
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: 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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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