GapMind for catabolism of small carbon sources

 

Alignments for a candidate for astD in Sinorhizobium fredii NGR234

Align N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized)
to candidate WP_012708927.1 NGR_RS23205 aldehyde dehydrogenase family protein

Query= curated2:Q2SXN9
         (487 letters)



>NCBI__GCF_000018545.1:WP_012708927.1
          Length = 477

 Score =  239 bits (611), Expect = 1e-67
 Identities = 171/472 (36%), Positives = 231/472 (48%), Gaps = 28/472 (5%)

Query: 6   IDGAWVDGAGPVFASRNPG-TNERVWEGASASADDVERAVASARRAFAAWSALDLDARCT 64
           I G WV G G   A+ NP  TN+ V E A ASA+D   A+A+A+ AF AWS   +  R  
Sbjct: 8   IAGEWVGGDG--IANVNPSNTNDVVGEYARASAEDASAAIAAAKAAFPAWSRSGILERHA 65

Query: 65  IVKRFAALLVERKEALATMIGRETGKPLWEARTEVASMAAKVDISITAYHERTGEKRAPM 124
           I+++ A  ++ RK+ L  ++ RE GK L E   E    +   D          GE    +
Sbjct: 66  ILRKTADEILARKDELGRLLSREEGKTLAEGIGETIRASQIFDFFAGECLRLAGETLPSV 125

Query: 125 ADGVAV-LRHRPHGVVAVFGPYNFPGHLPNGHIVPALIAGNTVVFKPSELAPGVARATVE 183
              + V +   P GVV +  P+NFP  +P   I PAL  GNTVVFKP+EL PG + A V+
Sbjct: 126 RPNIGVEISREPVGVVGIITPWNFPIAIPAWKIAPALAYGNTVVFKPAELVPGCSWAIVD 185

Query: 184 IWRDAGLPAGVLNLVQGEKD-TGVALANHRQIDGLFFTGSSDTG---TLLHKQFGGRPEI 239
           I   AGLP GVLNLV G+    G A+ +   +  + FTGS+ TG    L   +   +   
Sbjct: 186 ILHRAGLPKGVLNLVMGKGSVVGQAMLDSPDVQAITFTGSTGTGKRVALASVEHNRK--- 242

Query: 240 VLALEMGGNNPLVVAEVEDIDAAVHHAIQSAFLSAGQRCTCARRILVPRG-------AFG 292
              LEMGG NP VV +  D+  AV  A+ SAF S GQRCT + R++V  G       A G
Sbjct: 243 -FQLEMGGKNPFVVLDDADLSVAVEAAVNSAFFSTGQRCTASSRVIVTEGIHDKFVAAMG 301

Query: 293 DRFVARLADVASKITASVFDADPQPFMGAVISARAASRLVAAQARLVGLGASPIIEMKQR 352
           +R    + D A K    +     Q  +       A  +   A+    G       E+  R
Sbjct: 302 ERMKGLVVDDALKAGTHIGPVVDQSQLNQDTDYIAIGKQEGAKLAFGG-------ELISR 354

Query: 353 D-PALGFVNAAILDVTNVRELPDEEHFGPLAQIVRYTDLDDAIARANDTAFGLSAGLLAD 411
           D P      A   + TN   +  EE FGP+A ++R  D ++A+  ANDT FGLSAG+   
Sbjct: 355 DTPGFYLQPALFTEATNAMRISREEIFGPVAAVIRVKDYEEALNVANDTPFGLSAGIATT 414

Query: 412 DEQAWHTFRRAIRAGIVNWNRPTNGASSAAPFGG-AGRSGNHRPSAYYAADY 462
             +    F+R   AG+V  N PT G     PFGG  G S   R    YAA++
Sbjct: 415 SLKHATHFKRNSEAGMVMVNLPTAGVDFHVPFGGRKGSSHGPREQGKYAAEF 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: 514
Number of extensions: 17
Number of successful extensions: 3
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: 477
Length adjustment: 34
Effective length of query: 453
Effective length of database: 443
Effective search space:   200679
Effective search space used:   200679
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