GapMind for catabolism of small carbon sources

 

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

Align N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized)
to candidate WP_068168204.1 HTA01S_RS06375 betaine-aldehyde dehydrogenase

Query= curated2:Q2SXN9
         (487 letters)



>NCBI__GCF_001592305.1:WP_068168204.1
          Length = 485

 Score =  223 bits (568), Expect = 1e-62
 Identities = 168/470 (35%), Positives = 234/470 (49%), Gaps = 24/470 (5%)

Query: 5   FIDGAWVDGAGPVFASRNPGTNERVWEGASASADDVERAVASARRAFAAWSALDLDARCT 64
           FI+G  V+G G VF S NP T         A+ DDV RAV +A   FA WSA+    R  
Sbjct: 9   FINGQTVNGGGQVFESVNPATGRAYAVVHEATQDDVNRAVEAAGAGFALWSAMSATERGR 68

Query: 65  IVKRFAALLVERKEALATMIGRETGKPLWEART-EVASMAAKVDISITAYHERTGEKRAP 123
           I++R A +L ER   LA +  R+ GKP+ EA   +V S A  ++    A    TG++  P
Sbjct: 69  ILRRAADILRERNHELAALEVRDCGKPIQEALVVDVMSGADCIEYFAGAAATLTGQQY-P 127

Query: 124 MADGVAVLRHRPHGVVAVFGPYNFPGHLPNGHIVPALIAGNTVVFKPSELAPGVARATVE 183
           + +  A  R  P GV    G +N+P  +      PAL AGN ++FKPSEL P  A    E
Sbjct: 128 LKNAFAYTRKEPLGVCVGIGAWNYPIQIACWKSAPALAAGNAMIFKPSELTPATAVKLAE 187

Query: 184 IWRDAGLPAGVLNLVQGEKDTGVALANHRQIDGLFFTGSSDTGTLLHKQFGGRPEIVLAL 243
           ++ +AG+P GV N+VQG    G  LA H  +  +  TGS  TG  + +   G  + V  +
Sbjct: 188 VYLEAGVPPGVFNVVQGRGAVGAMLAAHPDVAKVSVTGSVPTGKRVMETAAGTLKRV-TM 246

Query: 244 EMGGNNPLVVAEVEDIDAAVHHAIQSAFLSAGQRCTCARRILVPRGAFGDRFVARLADVA 303
           E+GG +PL+V +  D++ AV  A+   F + G+ CT   R+ V RG    RF+ARL +  
Sbjct: 247 ELGGKSPLLVFDDADLEQAVAAAMMGNFYTQGEVCTNCTRVFVQRG-IAPRFLARLKE-- 303

Query: 304 SKITASVFD-ADPQPFMGAVISARAASRLV-------AAQARLVGLGASPIIEMKQRDPA 355
             +   V D  DP   +GA+IS    +R++       A  A LV  G    +E       
Sbjct: 304 RTLLLRVGDPTDPDTEIGALISEAHTARVMDYIASGQAEGATLVCGGERVAVE------G 357

Query: 356 LG--FVNAAIL-DVTNVRELPDEEHFGPLAQIVRYTDLDDAIARANDTAFGLSAGLLADD 412
           LG  FV   I  D  +   +  EE FGP+  ++ +    +AIARAN + F L+AG+   D
Sbjct: 358 LGDQFVAPTIFADCRDDMRIVREEIFGPVLSMLTFDTEAEAIARANQSRFSLAAGVFTTD 417

Query: 413 EQAWHTFRRAIRAGIVNWNRPTNGASSAAPFGGAGRSGNHRPSAYYAADY 462
            Q  H     IRAGI  W    N      PFGG G SG    ++  A D+
Sbjct: 418 LQRGHRVAAQIRAGIC-WINNYNITPIEMPFGGVGESGIGSENSMAALDH 466


Lambda     K      H
   0.320    0.134    0.402 

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: 447
Number of extensions: 23
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: 487
Length of database: 485
Length adjustment: 34
Effective length of query: 453
Effective length of database: 451
Effective search space:   204303
Effective search space used:   204303
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: 52 (24.6 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