GapMind for catabolism of small carbon sources

 

Alignments for a candidate for adh in Methylocapsa aurea KYG

Align Aldehyde dehydrogenase; EC 1.2.1.3 (characterized)
to candidate WP_051953139.1 DL86_RS09565 coniferyl aldehyde dehydrogenase

Query= SwissProt::P12693
         (483 letters)



>NCBI__GCF_000746085.1:WP_051953139.1
          Length = 476

 Score =  327 bits (837), Expect = 7e-94
 Identities = 182/456 (39%), Positives = 267/456 (58%), Gaps = 17/456 (3%)

Query: 35  GKFGIAERIAALNLLKETIQRREPEIIAALAADF-RKPASEVKLTEIFPVLQEINHAKRN 93
           G   + +R   L  LK  +     + +AA+ ADF  +   E  L E+ PV++ I +  RN
Sbjct: 28  GPPSLKQRRGDLMRLKGALLAHREDFVAAINADFGHRSRQETSLLELSPVIEGIKYLHRN 87

Query: 94  LKDWMKPRRVRAALSVAGTRAGLRYEPKGVCLIIAPWNYPFNLSFGPLVSALAAGNSVVI 153
           L  WM+P R + +         + Y+P GV  +I+PWNYP  L+  PL +ALAAGN V+I
Sbjct: 88  LALWMRPERRKVSFHFFPGSTRVLYQPLGVVGVISPWNYPVALALMPLATALAAGNRVMI 147

Query: 154 KPSELTPHTATLIGSIVREAFSVDLVAVVEGDAAVSQELLALPFDHIFFTGSPRVGKLVM 213
           KPSE+TP T+ L+ +++ E FS+D  AV  G+A V     ALPFDH+ FTGS  VG+ VM
Sbjct: 148 KPSEITPATSALMSAVLGEIFSLDQAAVATGEADVGMAFAALPFDHLVFTGSTPVGRSVM 207

Query: 214 EAASKTLASVTLELGGKSPTIIGPTANLPKAARNIVWGKFSNNGQTCIAPDHVFVHRCIA 273
            AAS  L  VTLELGGKSP I+   + L   AR I +GK +N GQTCIAPD+V      A
Sbjct: 208 RAASDNLVPVTLELGGKSPVIVERGSCLKTTARRIAYGKLANGGQTCIAPDYVL---AAA 264

Query: 274 QKFNEIL---VKEIVRVYGKDFAAQRRSADYCRIVNDQHFNRINKLLTDAKAKGAKILQG 330
           Q+ N+ +     E+ ++Y  D AA   + DY  I+ND H+ R+  LL DA+AKGA++++ 
Sbjct: 265 QEINDFVAAYAAEVEKLY-PDIAA---NPDYTSIINDHHYARLVGLLDDARAKGARVIEI 320

Query: 331 GQVD-----ATERLVVPTVLSNVTAAMDINHEEIFGPLLPIIEYDDIDSVIKRVNDGDKP 385
           G           R + P ++   T  M++  EEIFGP+LP+I Y  ++  +  VN   +P
Sbjct: 321 GAAPKEGERTNARTLAPAIVLGATDGMNVMKEEIFGPILPVIPYARLEEAVAYVNARPRP 380

Query: 386 LALYVFSEDKQFVNNIVARTSSGSVGVNLSVVHFLHPNLPFGGVNNSGIGSAHGVYGFRA 445
           LALY F  D      ++ART+SG V +N +++H+   ++PFGGV  SG+G+ HG  GF+ 
Sbjct: 381 LALYFFGPDGPGRRMVLARTTSGGVSINETILHYAQDDIPFGGVGASGMGAYHGHEGFKT 440

Query: 446 FSHEKPVLID-KFSITHWLFPPYTKKVKQLIGITVK 480
            SH + V    K ++T  + PP+ K  ++L+   ++
Sbjct: 441 LSHSRGVFEQAKVNLTDVVRPPFGKLFERLVDFLLR 476


Lambda     K      H
   0.320    0.136    0.395 

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: 534
Number of extensions: 21
Number of successful extensions: 3
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: 483
Length of database: 476
Length adjustment: 34
Effective length of query: 449
Effective length of database: 442
Effective search space:   198458
Effective search space used:   198458
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 51 (24.3 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