GapMind for catabolism of small carbon sources

 

Alignments for a candidate for astD in Streptomyces kebangsaanensis SUK12

Align N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized)
to candidate WP_073948994.1 RH94_RS20650 aldehyde dehydrogenase family protein

Query= curated2:B0T8I8
         (484 letters)



>NCBI__GCF_001906585.1:WP_073948994.1
          Length = 462

 Score =  198 bits (503), Expect = 4e-55
 Identities = 163/455 (35%), Positives = 218/455 (47%), Gaps = 30/455 (6%)

Query: 4   GLFIDGVWRAGAGAQATSVDPTTGEVIWRQATASTAE-VAAAVEAARKAFPAWADRSREE 62
           G++IDG WR  AG  A  V     E +     A TAE V AAV AAR A P WA     E
Sbjct: 6   GMYIDGAWRPAAGRDAIEVVNPADEQVIATVPAGTAEDVDAAVRAARAALPGWAATPPAE 65

Query: 63  RIAVLRRYKDVLVARTGTFAEALSRETGKALWETKAELGSMAGKVEASIKAYDERTGEHA 122
           R A L   +DVLVAR    AE ++ E G  L  ++A     AG   A   +Y +    +A
Sbjct: 66  RAARLTALRDVLVARKDEIAETVTAELGSPLAFSQAV---HAGVPIAVAGSYADLAATYA 122

Query: 123 NDMAFGRAVLRHRAHGVMAVLGPFNFPGHLPNGHIVPALLAGDTVVFKPSEETPLAGQLL 182
            +   G + + H   GV+  + P+N+P H       PAL AG T+V KP+E+TPL  QL 
Sbjct: 123 FEEKVGNSTVHHEPVGVVGAITPWNYPLHQIVAKAAPALAAGCTIVLKPAEDTPLTAQLF 182

Query: 183 VEALEEAGVPAGVINLVQG-GREVGQALIDQ-EIDGLLFTGSAAAGAFFRRHFADRPDVI 240
            EA  EAG+PAGV+NLV G G   GQAL +  ++D + FTGS A G   RR  A     +
Sbjct: 183 AEAAHEAGIPAGVLNLVTGLGPVAGQALAEHPDVDLVSFTGSTAVG---RRIGATAGAAV 239

Query: 241 --LALELGGNNPLVVWDAGDPEAVAALIVQSAFITTGQRCSCARRLIVSDDAAGRAV-ID 297
             +ALELGG +  V+  + D      + V +    +GQ CS   R++V  D    AV + 
Sbjct: 240 KRVALELGGKSANVILPSADLARAVNVGVANVMSNSGQTCSAWTRMLVHRDQYDEAVELA 299

Query: 298 AVAALSERLVIGP-WNGGQEPFMGPLISDRAA--AMALAGAKAMPGQTLRAMTSVDGLSR 354
           A AA      IGP  N  Q   +   I    A  A  +AG    P +             
Sbjct: 300 ATAAAKYGDRIGPVVNAKQRARVRGYIEKGIAEGARLVAGGPEAPCE-----------KG 348

Query: 355 AFVSPGL-VDVTGE-TVPDEELFAPLLQVRRVGSFEEAIAAANATRYGLSAGLVSNETAH 412
            FVSP +  DVT + TV  EE+F P+L + R    ++A+  AN T YGL+  + + +   
Sbjct: 349 YFVSPTVFADVTPDMTVAQEEIFGPVLSILRYDDEDDALRIANGTVYGLAGAVWAADETE 408

Query: 413 WDRFLTRIRAGVVNWNRPTTGAAGTMPFGGLGNSG 447
              F  R+  G V+ N          PFGG   SG
Sbjct: 409 AVAFARRMDTGQVDINGGRFNPLA--PFGGYKQSG 441


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: 546
Number of extensions: 30
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: 484
Length of database: 462
Length adjustment: 33
Effective length of query: 451
Effective length of database: 429
Effective search space:   193479
Effective search space used:   193479
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: 51 (24.3 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