GapMind for catabolism of small carbon sources

 

Alignments for a candidate for patD in Hydrogenophaga taeniospiralis CCUG 15921 NBRC 102512

Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate WP_068168204.1 HTA01S_RS06375 betaine-aldehyde dehydrogenase

Query= BRENDA::P77674
         (474 letters)



>NCBI__GCF_001592305.1:WP_068168204.1
          Length = 485

 Score =  346 bits (887), Expect = 1e-99
 Identities = 191/472 (40%), Positives = 275/472 (58%), Gaps = 10/472 (2%)

Query: 7   INGELVSGEGEKQPVYNPATGDVLLEIAEASAEQVDAAVRAADAAFAEWGQTTPKVRAEC 66
           ING+ V+G G+     NPATG     + EA+ + V+ AV AA A FA W   +   R   
Sbjct: 10  INGQTVNGGGQVFESVNPATGRAYAVVHEATQDDVNRAVEAAGAGFALWSAMSATERGRI 69

Query: 67  LLKLADVIEENGQVFAELESRNCGKPLHSAFNDEIPAIVDVFRFFAGAARCLNGLAAGEY 126
           L + AD++ E     A LE R+CGKP+  A   ++ +  D   +FAGAA  L G    +Y
Sbjct: 70  LRRAADILRERNHELAALEVRDCGKPIQEALVVDVMSGADCIEYFAGAAATLTGQ---QY 126

Query: 127 -LEGHTSMIRRDPLGVVASIAPWNYPLMMAAWKLAPALAAGNCVVLKPSEITPLTALKLA 185
            L+   +  R++PLGV   I  WNYP+ +A WK APALAAGN ++ KPSE+TP TA+KLA
Sbjct: 127 PLKNAFAYTRKEPLGVCVGIGAWNYPIQIACWKSAPALAAGNAMIFKPSELTPATAVKLA 186

Query: 186 ELAKDI-FPAGVINILFGRGKTVGDPLTGHPKVRMVSLTGSIATGEHIISHTASSIKRTH 244
           E+  +   P GV N++ GRG  VG  L  HP V  VS+TGS+ TG+ ++   A ++KR  
Sbjct: 187 EVYLEAGVPPGVFNVVQGRG-AVGAMLAAHPDVAKVSVTGSVPTGKRVMETAAGTLKRVT 245

Query: 245 MELGGKAPVIVFDDADIEAVVEGVRTFGYYNAGQDCTAACRIYAQKGIYDTLVEKLGAAV 304
           MELGGK+P++VFDDAD+E  V       +Y  G+ CT   R++ Q+GI    + +L    
Sbjct: 246 MELGGKSPLLVFDDADLEQAVAAAMMGNFYTQGEVCTNCTRVFVQRGIAPRFLARLKERT 305

Query: 305 ATLKSGAPDDESTELGPLSSLAHLERVGKAVEEAKATGHIKVITGGEKRKGNG---YYYA 361
             L+ G P D  TE+G L S AH  RV   +   +A G   ++ GGE+    G    + A
Sbjct: 306 LLLRVGDPTDPDTEIGALISEAHTARVMDYIASGQAEG-ATLVCGGERVAVEGLGDQFVA 364

Query: 362 PTLLAGALQDDAIVQKEVFGPVVSVTPFDNEEQVVNWANDSQYGLASSVWTKDVGRAHRV 421
           PT+ A    D  IV++E+FGPV+S+  FD E + +  AN S++ LA+ V+T D+ R HRV
Sbjct: 365 PTIFADCRDDMRIVREEIFGPVLSMLTFDTEAEAIARANQSRFSLAAGVFTTDLQRGHRV 424

Query: 422 SARLQYGCTWVNTHFMLVSEMPHGGQKLSGYGKDMSLYGLEDYTVVRHVMVK 473
           +A+++ G  W+N + +   EMP GG   SG G + S+  L+ YT ++ V V+
Sbjct: 425 AAQIRAGICWINNYNITPIEMPFGGVGESGIGSENSMAALDHYTQLKTVYVE 476


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: 554
Number of extensions: 25
Number of successful extensions: 4
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: 485
Length adjustment: 34
Effective length of query: 440
Effective length of database: 451
Effective search space:   198440
Effective search space used:   198440
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 Apr 09 2024. 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