GapMind for catabolism of small carbon sources

 

Alignments for a candidate for patD in Lutibaculum baratangense AMV1

Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate WP_023433101.1 N177_RS14415 aldehyde dehydrogenase

Query= BRENDA::P77674
         (474 letters)



>NCBI__GCF_000496075.1:WP_023433101.1
          Length = 492

 Score =  318 bits (815), Expect = 3e-91
 Identities = 181/472 (38%), Positives = 266/472 (56%), Gaps = 7/472 (1%)

Query: 7   INGELVSGEGEKQPVYNPATGDVLLEIAEASAEQVDAAVRAADAAFAE--WGQTTPKVRA 64
           I+G    G        +PATG+    +  A+A  VD AVRAAD AF +  W + T   R 
Sbjct: 10  IDGAFCEGGAGSFESVDPATGEAWANMPAANAADVDRAVRAADRAFHDPSWSRLTATQRG 69

Query: 65  ECLLKLADVIEENGQVFAELESRNCGKPLHSAFNDEIPAIVDVFRFFAGAARCLNGLAAG 124
           + L +LAD++ EN Q  AELE+R+ GK +    + +I  + D +R++AG A  + G    
Sbjct: 70  KLLYRLADLVAENAQALAELETRDTGKIIRET-SAQIAYVADYYRYYAGLADKIEGAHLP 128

Query: 125 EYLEGHTSMIRRDPLGVVASIAPWNYPLMMAAWKLAPALAAGNCVVLKPSEITPLTALKL 184
                  + +RR+P+GVVA++ PWN  L ++A KL PALAAG  VVLK SE  P   L  
Sbjct: 129 IDKPDMETYLRREPIGVVAAVVPWNSQLFLSAVKLGPALAAGCTVVLKASEDGPAPLLAF 188

Query: 185 AELAKDI-FPAGVINILFGRGKTVGDPLTGHPKVRMVSLTGSIATGEHIISHTASSIKRT 243
           A L     FP GV+NIL G G   G  L  HP V  ++ TG  AT  HI+ H+A ++   
Sbjct: 189 ARLVDQAGFPPGVVNILTGFGDQCGSALASHPLVARIAFTGGPATARHIVRHSAENLAAV 248

Query: 244 HMELGGKAPVIVFDDADIEAVVEGVRTFGYYNAGQDCTAACRIYAQKGIYDTLVEKLGAA 303
            +ELGGK+PV+VF+DAD+++V   V    +   GQ C A  R+  Q+GI D L+E+L   
Sbjct: 249 TLELGGKSPVVVFEDADLDSVANAVVAGIFAATGQSCVAGSRLIVQRGIKDALLERLVQK 308

Query: 304 VATLKSGAPDDESTELGPLSSLAHLERVGKAVEEAKATGHIKVITGGEKRKG--NGYYYA 361
              ++ G P  + TE+GPL++   L  +   +  + A G  +++TGG +  G   G+Y+ 
Sbjct: 309 ARAIRIGDPQAQETEMGPLATARQLRHIEDVIARSLAAGG-RLVTGGGRPDGFPAGHYFE 367

Query: 362 PTLLAGALQDDAIVQKEVFGPVVSVTPFDNEEQVVNWANDSQYGLASSVWTKDVGRAHRV 421
           PT++         V++E+FGPV+SV  F+ E + V +AN + YGLAS V+T  + RAHR+
Sbjct: 368 PTIIDCDATTIPSVEEELFGPVLSVLGFEEETEAVEFANRTPYGLASGVFTASLTRAHRM 427

Query: 422 SARLQYGCTWVNTHFMLVSEMPHGGQKLSGYGKDMSLYGLEDYTVVRHVMVK 473
              ++ G  WVNT+  +   MP GG  LSG G++  L    DYT  + V ++
Sbjct: 428 IRAIRAGVVWVNTYRAVSPIMPFGGYGLSGSGREGGLDAALDYTRTKAVWIR 479


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: 597
Number of extensions: 23
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: 474
Length of database: 492
Length adjustment: 34
Effective length of query: 440
Effective length of database: 458
Effective search space:   201520
Effective search space used:   201520
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: 52 (24.6 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