GapMind for catabolism of small carbon sources

 

Alignments for a candidate for astD in Lutibaculum baratangense AMV1

Align N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized)
to candidate WP_023433101.1 N177_RS14415 aldehyde dehydrogenase

Query= curated2:B0T8I8
         (484 letters)



>NCBI__GCF_000496075.1:WP_023433101.1
          Length = 492

 Score =  199 bits (506), Expect = 2e-55
 Identities = 155/466 (33%), Positives = 222/466 (47%), Gaps = 16/466 (3%)

Query: 6   FIDGVWRAGAGAQATSVDPTTGEVIWRQATASTAEVAAAVEAARKAF--PAWADRSREER 63
           +IDG +  G      SVDP TGE       A+ A+V  AV AA +AF  P+W+  +  +R
Sbjct: 9   YIDGAFCEGGAGSFESVDPATGEAWANMPAANAADVDRAVRAADRAFHDPSWSRLTATQR 68

Query: 64  IAVLRRYKDVLVARTGTFAEALSRETGKALWETKAELGSMAGKVEASIKAYDERTGEHAN 123
             +L R  D++       AE  +R+TGK + ET A++  +A          D+  G H  
Sbjct: 69  GKLLYRLADLVAENAQALAELETRDTGKIIRETSAQIAYVADYYRYYAGLADKIEGAHLP 128

Query: 124 -DMAFGRAVLRHRAHGVMAVLGPFNFPGHLPNGHIVPALLAGDTVVFKPSEETPLAGQLL 182
            D       LR    GV+A + P+N    L    + PAL AG TVV K SE+ P      
Sbjct: 129 IDKPDMETYLRREPIGVVAAVVPWNSQLFLSAVKLGPALAAGCTVVLKASEDGPAPLLAF 188

Query: 183 VEALEEAGVPAGVINLVQG-GREVGQALIDQE-IDGLLFTGSAAAGAFFRRHFADRPDVI 240
              +++AG P GV+N++ G G + G AL     +  + FTG  A      RH A+    +
Sbjct: 189 ARLVDQAGFPPGVVNILTGFGDQCGSALASHPLVARIAFTGGPATARHIVRHSAENLAAV 248

Query: 241 LALELGGNNPLVVWDAGDPEAVAALIVQSAFITTGQRCSCARRLIVSDDAAGRAVIDAVA 300
             LELGG +P+VV++  D ++VA  +V   F  TGQ C    RLIV       A+++ + 
Sbjct: 249 -TLELGGKSPVVVFEDADLDSVANAVVAGIFAATGQSCVAGSRLIVQRGIKD-ALLERLV 306

Query: 301 ALSERLVIGPWNGGQEPFMGPLISDRAAAM---ALAGAKAMPGQTLRAMTSVDGLSRA-F 356
             +  + IG     QE  MGPL + R        +A + A  G+ +      DG     +
Sbjct: 307 QKARAIRIGD-PQAQETEMGPLATARQLRHIEDVIARSLAAGGRLVTGGGRPDGFPAGHY 365

Query: 357 VSPGLVDVTGETVP--DEELFAPLLQVRRVGSFEEAIAAANATRYGLSAGLVSNETAHWD 414
             P ++D    T+P  +EELF P+L V       EA+  AN T YGL++G+ +       
Sbjct: 366 FEPTIIDCDATTIPSVEEELFGPVLSVLGFEEETEAVEFANRTPYGLASGVFTASLTRAH 425

Query: 415 RFLTRIRAGVVNWNRPTTGAAGTMPFGGLGNSGNHRPSAYYAA-DY 459
           R +  IRAGVV W       +  MPFGG G SG+ R     AA DY
Sbjct: 426 RMIRAIRAGVV-WVNTYRAVSPIMPFGGYGLSGSGREGGLDAALDY 470


Lambda     K      H
   0.318    0.134    0.395 

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: 620
Number of extensions: 33
Number of successful extensions: 6
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: 484
Length of database: 492
Length adjustment: 34
Effective length of query: 450
Effective length of database: 458
Effective search space:   206100
Effective search space used:   206100
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: 52 (24.6 bits)

This GapMind analysis is from Sep 24 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