GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gabD in Limnohabitans curvus MWH-C5

Align succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) (characterized)
to candidate WP_108402515.1 B9Z44_RS11745 NAD-dependent succinate-semialdehyde dehydrogenase

Query= BRENDA::P25526
         (482 letters)



>NCBI__GCF_003063475.1:WP_108402515.1
          Length = 492

 Score =  596 bits (1536), Expect = e-175
 Identities = 288/482 (59%), Positives = 364/482 (75%), Gaps = 7/482 (1%)

Query: 3   LNDSNLFRQQALINGEWLDANNGEAIDVTNPANGDKLGSVPKMGADETRAAIDAANRALP 62
           LND  L +  ALING W+        DV +PA G KL  V  +G  +  AAIDAAN A P
Sbjct: 11  LNDPTLLKTDALINGHWV--KGASRFDVHDPATGKKLADVANLGPADASAAIDAANAAWP 68

Query: 63  AWRALTAKERATILRNWFNLMMEHQDDLARLMTLEQGKPLAEAKGEISYAASFIEWFAEE 122
           AWR  T KER+ ILR WF+L+M HQ+DL R+MT EQGKP AEAKGE+ Y ASF+EWFAEE
Sbjct: 69  AWRNKTGKERSIILRKWFDLLMAHQEDLGRIMTAEQGKPFAEAKGEVVYGASFVEWFAEE 128

Query: 123 GKRIYGDTIPGHQADKRLIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVLKPA 182
            KR+ G+T+P    ++RL+V+KQPIGV AAITPWNFP AMITRK  PALAAGC +V+KPA
Sbjct: 129 AKRVNGETLPQFDNNRRLMVLKQPIGVCAAITPWNFPLAMITRKVAPALAAGCPVVIKPA 188

Query: 183 SQTPFSALALAELAIRAGVPAGVFNVVTGSAG---AVGNELTSNPLVRKLSFTGSTEIGR 239
              P +ALA AELAIRAG+P GV N++T  +    A+G    S+ +VR +SFTGSTE+GR
Sbjct: 189 ELPPLTALAAAELAIRAGIPDGVLNILTADSDNSIAIGKVFCSSDIVRHISFTGSTEVGR 248

Query: 240 QLMEQCAKDIKKVSLELGGNAPFIVFDDADLDKAVEGALASKFRNAGQTCVCANRLYVQD 299
            LM Q A  IKK++LELGGNAPFIVFDDAD+D AVEGA+ASK+RNAGQTCVCANR+YVQD
Sbjct: 249 ILMAQSAPSIKKLALELGGNAPFIVFDDADIDSAVEGAMASKYRNAGQTCVCANRIYVQD 308

Query: 300 GVYDRFAEKLQQAVSKLHIGDGLDNGVTIGPLIDEKAVAKVEEHIADALEKGARVVCGGK 359
            VYD F +K    V  L +G+G ++GVT GPLI++ AV KVE H+ DAL KG +++ GG 
Sbjct: 309 AVYDEFVQKFAAKVKALKVGNGFEDGVTQGPLIEDAAVDKVERHVQDALHKGGKLITGG- 367

Query: 360 AHERGGNFFQPTILVDVPANAKVSKEETFGPLAPLFRFKDEADVIAQANDTEFGLAAYFY 419
            H+  G FF+PT++ D  A+   ++EETFGP AP+FRF  + + I  AN+TEFGLA+YFY
Sbjct: 368 -HKLTGQFFEPTVIADARADMLCAREETFGPFAPVFRFHKDQEAIDAANNTEFGLASYFY 426

Query: 420 ARDLSRVFRVGEALEYGIVGINTGIISNEVAPFGGIKASGLGREGSKYGIEDYLEIKYMC 479
           +RD+ R++RV EALEYG+VGIN GII++E  PFGG+K SGLGREGS +G+++Y+E+KY+C
Sbjct: 427 SRDIGRIYRVSEALEYGMVGINVGIIASEHVPFGGVKQSGLGREGSSHGMDEYVEMKYLC 486

Query: 480 IG 481
           +G
Sbjct: 487 LG 488


Lambda     K      H
   0.318    0.135    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: 715
Number of extensions: 23
Number of successful extensions: 4
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: 482
Length of database: 492
Length adjustment: 34
Effective length of query: 448
Effective length of database: 458
Effective search space:   205184
Effective search space used:   205184
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