GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dddA in Azospirillum thiophilum BV-S

Align 3-hydroxypropionate dehydrogenase (EC 1.1.1.59) (characterized)
to candidate WP_045583809.1 AL072_RS25745 NAD(P)-binding protein

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



>NCBI__GCF_001305595.1:WP_045583809.1
          Length = 552

 Score =  393 bits (1010), Expect = e-114
 Identities = 230/550 (41%), Positives = 319/550 (58%), Gaps = 26/550 (4%)

Query: 36  FDYIVVGAGTAGCLLANRLSADPANRVLLIEAGGRDNYHWIHIPVGYLYCINNPRTDWRF 95
           +DYIVVGAG AGC LA RL+ D  +RVLL+EAGGRD   WIHIP+G    + NP+  W+F
Sbjct: 4   YDYIVVGAGAAGCALAARLTEDGRHRVLLLEAGGRDANIWIHIPLGVGKLLQNPKYVWQF 63

Query: 96  RTEPDPGLNGRSLIYPRGKTLGGCSSINGMLYLRGQARDYDGWAELTGDDAWRWDNCLPD 155
            TEP+P L+G+ + +PRGK +GG SS+NGM+Y+RG   +YD W  L G+  W + + LP 
Sbjct: 64  MTEPEPALHGQRIYWPRGKVMGGSSSVNGMVYVRGDPEEYDHWRAL-GNPGWGYADLLPY 122

Query: 156 FMRHEDHYRLDEGGDADPDHYKFHGHGGEWRIEKQRLKW--QVLAD-FATAAVEAGVPRT 212
           F R ED+         DP    + G GG  +I   R  W    L+D +  A +EAG+P  
Sbjct: 123 FKRMEDY------PQGDP---AYRGRGGPMKI-VNRGAWDPDPLSDAYLAACIEAGIPPN 172

Query: 213 RDFNRGDNEGVDAFEVNQRSGWRWNASKAFLRGVEQRGNLTVWHSTQVLKLDFASGEGSE 272
            D+N    EG    + N R+G R +++  +L    +R NL +  + Q  ++ F       
Sbjct: 173 EDYNATTLEGAAYLQQNGRNGRRCSSAAGYLATARKRPNLRIETNAQATRVLFQG----- 227

Query: 273 PRCCGVTVERAGKKVVTTARCEVVLSAGAIGSPQLLQLSGIGPTALLAEHAIPVVADLPG 332
            R  GV   + G      AR EV+LSAG++ SPQLL+LSGIG    L    IPVV  LPG
Sbjct: 228 TRAVGVEYRQDGILREARARGEVLLSAGSVQSPQLLELSGIGDERRLRALGIPVVTHLPG 287

Query: 333 VGENLQDHLQIRSIYKVKGAKTLNTMANSLIGKAKIGLEYILKRSGPMSMAPSQLCIFTR 392
           VGE+L DHLQ+R  ++     T+N M +S + +  +GLEY+L R G +S   S +    R
Sbjct: 288 VGESLLDHLQVRFTFECTRPITINDMIHSPVRRMMVGLEYVLFRRGLLSTTSSTVHAIAR 347

Query: 393 SSKEYEHPNLEYHVQPLS-LEAFGQP----LHDFPAITASVCNLNPTSRGTVRIKSGNPR 447
           +  E   P+++  +  +S  + + +        +P  +  V  L P SRG++ I+S +P 
Sbjct: 348 TRPELPRPDVKIQLAQISGKDRYSRSKELGTDRYPGFSIGVFKLRPESRGSLHIRSADPL 407

Query: 448 QAPAISPNYLSTEEDRQVAADSLRVTRHIASQPAFAKYDPEEFKPGVQYQSDEDLARLAG 507
           + P I PNYL   +D Q   D+ ++ R IA+QPAFA     E +PG     DEDL   A 
Sbjct: 408 EPPEIRPNYLGHPKDEQTYVDAFKLIRRIAAQPAFAPLMAGERRPGPDTTRDEDLVDYAR 467

Query: 508 DIGTTIFHPVGTAKMGRDDDPMAVVDSHLRVRGVTGLRVVDASIMPTITSGNTNSPTLMI 567
             G T +HP+ + +MG DD  MAVVD+ LRVRGV GLRVVDASIMPT+ S NTN+P +MI
Sbjct: 468 RTGQTSWHPISSCRMGTDD--MAVVDARLRVRGVQGLRVVDASIMPTMASPNTNAPAIMI 525

Query: 568 AEKAAGWILK 577
            EK A  +L+
Sbjct: 526 GEKGADLVLE 535


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: 935
Number of extensions: 51
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: 552
Length adjustment: 36
Effective length of query: 543
Effective length of database: 516
Effective search space:   280188
Effective search space used:   280188
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 24 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