GapMind for catabolism of small carbon sources

 

Alignments for a candidate for astD in Sinorhizobium meliloti 1021

Align N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized)
to candidate SM_b20891 SM_b20891 dehydrogenase

Query= curated2:Q2SXN9
         (487 letters)



>FitnessBrowser__Smeli:SM_b20891
          Length = 477

 Score =  238 bits (608), Expect = 3e-67
 Identities = 172/466 (36%), Positives = 236/466 (50%), Gaps = 16/466 (3%)

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

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

Query: 125 ADGVAV-LRHRPHGVVAVFGPYNFPGHLPNGHIVPALIAGNTVVFKPSELAPGVARATVE 183
             G+ V +   P GVV +  P+NFP  +P   + PAL  GNT+VFKP+EL PG + A V+
Sbjct: 126 RPGIGVEITREPAGVVGIITPWNFPIAIPAWKLAPALCYGNTIVFKPAELVPGCSWAIVD 185

Query: 184 IWRDAGLPAGVLNLVQGEKD-TGVALANHRQIDGLFFTGSSDTGTLLHKQFGGRPEIVLA 242
           I   AGLP GVLNLV G+    G A+ +   +  + FTGS+ TG  +             
Sbjct: 186 ILHRAGLPKGVLNLVMGKGSVVGQAMLDSPDVQAITFTGSTATGKRV-AVASVEHNRKYQ 244

Query: 243 LEMGGNNPLVVAEVEDIDAAVHHAIQSAFLSAGQRCTCARRILVPRGAFGDRFVARLADV 302
           LEMGG NP VV +  D+  AV  A+ SAF S GQRCT + RI+V  G   DRFVA + + 
Sbjct: 245 LEMGGKNPFVVLDDADLSVAVEAAVNSAFFSTGQRCTASSRIIVTEG-IHDRFVAAMGE- 302

Query: 303 ASKITASVFD--ADPQPFMGAVISARAASRLV--AAQARLVGLGASPIIEMKQRD-PALG 357
             +I   V D    P   +G V+     ++     A  +  G   +   E+  RD P   
Sbjct: 303 --RIKGLVVDDALKPGTHIGPVVDQSQLNQDTDYIAIGKQEGAKLAFGGEVISRDTPGFY 360

Query: 358 FVNAAILDVTNVRELPDEEHFGPLAQIVRYTDLDDAIARANDTAFGLSAGLLADDEQAWH 417
              A   + TN   +  EE FGP+A ++R  D D+A+A ANDT FGLS+G+     +   
Sbjct: 361 LQPALFTEATNEMRISREEIFGPVAAVIRVKDYDEALAVANDTPFGLSSGIATTSLKHAT 420

Query: 418 TFRRAIRAGIVNWNRPTNGASSAAPFGGAGRSG-NHRPSAYYAADY 462
            F+R   AG+V  N PT G     PFGG   S    R    YAA++
Sbjct: 421 HFKRNAEAGMVMVNLPTAGVDFHVPFGGRKASSYGPREQGKYAAEF 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: 527
Number of extensions: 22
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 Sep 17 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