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_068173812.1 HTA01S_RS16360 aldehyde dehydrogenase family protein

Query= curated2:Q2SXN9
         (487 letters)



>NCBI__GCF_001592305.1:WP_068173812.1
          Length = 483

 Score =  217 bits (553), Expect = 6e-61
 Identities = 158/463 (34%), Positives = 219/463 (47%), Gaps = 8/463 (1%)

Query: 5   FIDGAWVDGAGPVFASRNPGTNERVWEGASASADDVERAVASARRAFAAWSALDLDARCT 64
           FI+G W  G     ++    T E V E A A  +  E A+ +A  A   WS      R  
Sbjct: 13  FINGRWEIGTTTGVSTNPSDTREVVAEYARADRNQTELAIRAAADALPHWSQSSPQRRAD 72

Query: 65  IVKRFAALLVERKEALATMIGRETGKPLWEARTEVASMAAKVDISITAYHERTGEKRAPM 124
           ++ +  + L+ RK+ L  ++ RE GK L E   EVA                 GE  A +
Sbjct: 73  VLDQIGSELLARKDELGALLAREEGKTLPEGVGEVARAGQIFKFFAGEALRIPGEVIASV 132

Query: 125 ADGVAV-LRHRPHGVVAVFGPYNFPGHLPNGHIVPALIAGNTVVFKPSELAPGVARATVE 183
             GV V +   P GVV +  P+NFP  +P   I PAL  GNTVVFKP+EL P    A  E
Sbjct: 133 RPGVRVDVTREPVGVVGIIAPWNFPFAIPAWKIAPALAYGNTVVFKPAELVPACGWALAE 192

Query: 184 IWRDAGLPAGVLNLVQGE-KDTGVALANHRQIDGLFFTGSSDTGTLLHKQFGGRPEIVLA 242
           I    GLPAGV NLV G  ++ G  L +H  ++ L FTGS  TG  + K    R    + 
Sbjct: 193 IISRCGLPAGVFNLVMGSGREVGQTLVDHPLVNALSFTGSVSTGERILKAATAR-RAKVQ 251

Query: 243 LEMGGNNPLVVAEVEDIDAAVHHAIQSAFLSAGQRCTCARRILVPRGAFGDRFVARLADV 302
           LEMGG NPLVV    D+D AV  A+Q ++ S GQRCT + R++V +    D FVA+L   
Sbjct: 252 LEMGGKNPLVVLADADLDQAVDCALQGSYFSTGQRCTASSRLIV-QAQVHDAFVAKLRQR 310

Query: 303 ASKITASVFDADPQPFMGAVISARAASRLVAAQARLVGLGASPII--EMKQRDPALGFVN 360
            S +       +    MG V+      + +A        GA  +   ++ QR     +++
Sbjct: 311 LSTLKVG-HALERGTEMGPVVDRAQLEQNLAYIEIARNEGAEHVWGGDLLQRPTPGHYMS 369

Query: 361 AAILDVTNVRELPDEEHFGPLAQIVRYTDLDDAIARANDTAFGLSAGLLADDEQAWHTFR 420
            A+        +  EE FGP+A ++R  D + A+  ANDT FGL AG+     +    F+
Sbjct: 370 PALFLAKPEHRVAREEIFGPVACVLRADDYEHALVLANDTPFGLCAGICTTSLKYAMHFK 429

Query: 421 RAIRAGIVNWNRPTNGASSAAPFGGAGRSGN-HRPSAYYAADY 462
           R    G+   N PT G     PFGG   S +  R    YA ++
Sbjct: 430 RHAEVGMTMVNLPTAGVDFHVPFGGRKESSHGSREQGRYAVEF 472


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: 549
Number of extensions: 26
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: 487
Length of database: 483
Length adjustment: 34
Effective length of query: 453
Effective length of database: 449
Effective search space:   203397
Effective search space used:   203397
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