GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dddA in Marinobacter algicola DG893

Align 3-hydroxypropionate dehydrogenase (EC 1.1.1.59) (characterized)
to candidate WP_040474614.1 MDG893_RS13420 FAD-binding protein

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



>NCBI__GCF_000170835.1:WP_040474614.1
          Length = 558

 Score =  900 bits (2326), Expect = 0.0
 Identities = 432/548 (78%), Positives = 481/548 (87%), Gaps = 1/548 (0%)

Query: 33  THAFDYIVVGAGTAGCLLANRLSADPANRVLLIEAGGRDNYHWIHIPVGYLYCINNPRTD 92
           T  FDYIVVGAGTAGCLLANRLSA+P NRVLLIEAGG+D YHWIHIPVGYLYCI+NPRTD
Sbjct: 11  TPEFDYIVVGAGTAGCLLANRLSANPDNRVLLIEAGGKDTYHWIHIPVGYLYCIDNPRTD 70

Query: 93  WRFRTEPDPGLNGRSLIYPRGKTLGGCSSINGMLYLRGQARDYDGWAELTGDDAWRWDNC 152
           WRFRT+P PGLNGRSLIYPRGKTLGGCSSINGMLY+RGQARDY+ WA++TGDDAW W+NC
Sbjct: 71  WRFRTDPVPGLNGRSLIYPRGKTLGGCSSINGMLYIRGQARDYNHWADVTGDDAWNWENC 130

Query: 153 LPDFMRHEDHYRLDEGGDADPDHYKFHGHGGEWRIEKQRLKWQVLADFATAAVEAGVPRT 212
           LP FMRHEDHYRLDEGG+AD DH KFHGHGGEWRIE QRLKWQVL DFA AAV+AGVPRT
Sbjct: 131 LPYFMRHEDHYRLDEGGNADADHNKFHGHGGEWRIEHQRLKWQVLEDFAEAAVQAGVPRT 190

Query: 213 RDFNRGDNEGVDAFEVNQRSGWRWNASKAFLRGVEQRGNLTVWHSTQVLKLDFASGEGSE 272
            DFNRGDNEGVD FEVNQRSGWRWN SKAFLR    RGNLT+WHS QVL L+    +G +
Sbjct: 191 YDFNRGDNEGVDYFEVNQRSGWRWNTSKAFLRSATNRGNLTLWHSAQVLALNMEPTDGGQ 250

Query: 273 PRCCGVTVERA-GKKVVTTARCEVVLSAGAIGSPQLLQLSGIGPTALLAEHAIPVVADLP 331
           P C GV V +A G + +  A  EV+LSAG+IGSPQLLQLSGIGP  LL + +IPVVADLP
Sbjct: 251 PHCTGVRVAKANGNETLALAAKEVILSAGSIGSPQLLQLSGIGPADLLEQLSIPVVADLP 310

Query: 332 GVGENLQDHLQIRSIYKVKGAKTLNTMANSLIGKAKIGLEYILKRSGPMSMAPSQLCIFT 391
           GVGENLQDHLQIRS+YK+ GAKTLNTM +SL GKA+IGLEY+ KRSGPMSMAPSQLC FT
Sbjct: 311 GVGENLQDHLQIRSVYKLHGAKTLNTMIHSLFGKAQIGLEYLAKRSGPMSMAPSQLCAFT 370

Query: 392 RSSKEYEHPNLEYHVQPLSLEAFGQPLHDFPAITASVCNLNPTSRGTVRIKSGNPRQAPA 451
           RSS +Y++ N++YHVQPLSL+AFGQPLH FPAITASVCNLNP+SRGTVRI S + R AP+
Sbjct: 371 RSSDDYDYANIQYHVQPLSLDAFGQPLHTFPAITASVCNLNPSSRGTVRIHSRDARHAPS 430

Query: 452 ISPNYLSTEEDRQVAADSLRVTRHIASQPAFAKYDPEEFKPGVQYQSDEDLARLAGDIGT 511
           I+PNYL+T EDR+VAADSLRVTR IA Q AF+KY PEE+KPGV+YQ+D++LARLAGDIGT
Sbjct: 431 IAPNYLNTAEDRKVAADSLRVTRRIAQQEAFSKYQPEEYKPGVEYQTDDELARLAGDIGT 490

Query: 512 TIFHPVGTAKMGRDDDPMAVVDSHLRVRGVTGLRVVDASIMPTITSGNTNSPTLMIAEKA 571
           TIFHPVGT +MGR +D MAVVDSHL+VRGV GLRVVDA IMPTITSGNTNSPTLMIAEKA
Sbjct: 491 TIFHPVGTTRMGRANDEMAVVDSHLQVRGVLGLRVVDAGIMPTITSGNTNSPTLMIAEKA 550

Query: 572 AGWILKSQ 579
           A WIL  +
Sbjct: 551 ANWILNDE 558


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: 1098
Number of extensions: 35
Number of successful extensions: 2
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: 558
Length adjustment: 36
Effective length of query: 543
Effective length of database: 522
Effective search space:   283446
Effective search space used:   283446
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