GapMind for catabolism of small carbon sources

 

Alignments for a candidate for patD in Dyella japonica UNC79MFTsu3.2

Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate N515DRAFT_3729 N515DRAFT_3729 aminomuconate-semialdehyde/2-hydroxymuconate-6-semialdehyde dehydrogenase

Query= BRENDA::P77674
         (474 letters)



>FitnessBrowser__Dyella79:N515DRAFT_3729
          Length = 483

 Score =  341 bits (875), Expect = 3e-98
 Identities = 201/477 (42%), Positives = 278/477 (58%), Gaps = 10/477 (2%)

Query: 6   LINGELVSGEGEKQ-PVYNPATGDVLLEIAEASAEQVDAAVRAADAAFAEWGQTTPKVRA 64
           LI+G L +   E+   V+ PATG+V     E+S   VDAAV AA AA   W  T  + RA
Sbjct: 9   LIDGRLQAPRQERWLEVFEPATGEVFAHCPESSFADVDAAVAAAVAAAPGWAATPSEQRA 68

Query: 65  ECLLKLADVIEENGQVFAELESRNCGKPLHSAFNDEIPAIVDVFRFFAGAARCLNGLAAG 124
             L +LAD+IE     FA LESR+ GKPL  A + +IP  V   R+FA A    +  +  
Sbjct: 69  RLLQRLADLIEARLDEFAALESRDSGKPLSLARSLDIPRAVSNLRYFAAAIVPWSSESHA 128

Query: 125 EYLEGHTSMIRRDPLGVVASIAPWNYPLMMAAWKLAPALAAGNCVVLKPSEITPLTALKL 184
             L G  +   R PLGVVA I+PWN PL +  WK+APALAAGN VV KPSEITP TA  L
Sbjct: 129 MEL-GAINYTLRQPLGVVACISPWNLPLYLFTWKIAPALAAGNAVVAKPSEITPCTAALL 187

Query: 185 AELAKDI-FPAGVINILFGRGKTVGDPLTGHPKVRMVSLTGSIATGEHIISHTASSIKRT 243
            EL+ +  FP GV+NI+ GRG  VG  L  H  V+ VS TGS  TG  I +  A   K+ 
Sbjct: 188 GELSIEAGFPPGVLNIVQGRGPEVGQALVEHRDVKAVSFTGSTRTGAQIAAAAAPRFKKL 247

Query: 244 HMELGGKAPVIVFDDADI-EAVVEGVRTFGYYNAGQDCTAACRIYAQKGIYDTLVEKLGA 302
            +ELGGK P IVF DAD+ +A ++ +   G+ N G+ C    R+  Q+ IYD   E+  A
Sbjct: 248 SLELGGKNPAIVFADADLSDANLDTIVRSGFANQGEICLCGSRLLVQRSIYDAFRERYLA 307

Query: 303 AVATLKSGAPDDESTELGPLSSLAHLERVGKAVEEAKATGHIKVITGGEKRK-----GNG 357
            V  L+ G P + +T+LG L S  H ++V   + +A+A G  +V+ GG+          G
Sbjct: 308 KVRALRVGDPREAATDLGALVSREHFDKVTGCIAQARAEGG-RVLCGGDALALPGPLAGG 366

Query: 358 YYYAPTLLAGALQDDAIVQKEVFGPVVSVTPFDNEEQVVNWANDSQYGLASSVWTKDVGR 417
           +Y APT++ G   + A  Q+E+FGPVV++ PFD+E Q +  AN + YGLA+S+WT D+ R
Sbjct: 367 WYVAPTVIEGLGPETATNQQEIFGPVVTLIPFDDEAQALAIANGTGYGLAASLWTTDLSR 426

Query: 418 AHRVSARLQYGCTWVNTHFMLVSEMPHGGQKLSGYGKDMSLYGLEDYTVVRHVMVKH 474
           AHR  A+L +G  W+N   +     P GG K SG G++  +  L  +T  +++ +++
Sbjct: 427 AHRFGAQLDFGIVWINCWLLRDLRTPFGGAKQSGVGREGGVEALRFFTEPKNICIRY 483


Lambda     K      H
   0.317    0.134    0.397 

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: 541
Number of extensions: 29
Number of successful extensions: 5
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: 474
Length of database: 483
Length adjustment: 34
Effective length of query: 440
Effective length of database: 449
Effective search space:   197560
Effective search space used:   197560
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: 51 (24.3 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