GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gabD in Pseudomonas litoralis 2SM5

Align Succinate-semialdehyde dehydrogenase; SsaDH; EC 1.2.1.16 (characterized)
to candidate WP_090273153.1 BLU11_RS09735 NAD-dependent succinate-semialdehyde dehydrogenase

Query= SwissProt::Q8GAI8
         (450 letters)



>NCBI__GCF_900105005.1:WP_090273153.1
          Length = 493

 Score =  424 bits (1091), Expect = e-123
 Identities = 211/444 (47%), Positives = 300/444 (67%)

Query: 2   LATLASATSEDAVAALEAACAAQTSWARTAPRVRAEILRRAFDLVTARSEDFALLMTLEM 61
           +ATL S + E A+  +  A  A   WA+T PR R++ L  A+ ++ A  E  A +++ EM
Sbjct: 45  IATLPSLSPEQAIEEVAIAYQAGRDWAKTTPRHRSDTLHNAYLVLIANKERLAYVISREM 104

Query: 62  GKPLAEARGEVAYGAEFLRWFSEETVRDYGRYLTTPEGKNKILVQHKPVGPCLLITPWNF 121
           GK LAEA+GEV Y A+++RW+++E +R  G Y   P G + IL +  PVG  LLI PWNF
Sbjct: 105 GKTLAEAQGEVQYAADYVRWYADELLRPAGGYRDNPAGGSTILTKRAPVGLALLIAPWNF 164

Query: 122 PLAMATRKVAPAVAAGCTMVLKPAKLTPLTSQLFAQTMMEAGLPAGVLNVVSSSSASGIS 181
           P+AM TRK+APA+AAGC  V+KPA LTPLT+ L    + EAG+P  ++ VV+++ +S  S
Sbjct: 165 PMAMITRKIAPAIAAGCASVIKPAGLTPLTTLLTVDLLAEAGVPRELMRVVTTTQSSAFS 224

Query: 182 GPLLKDSRLRKVSFTGSTPVGKRLMSDASRHVLRTSMELGGNAPFVVFEDADLDKAVEGA 241
             +L D R+RK+SFTGST VG  LM  A+++++++SMELGGNAP +VF+DADL++AVEGA
Sbjct: 225 EAVLADPRVRKISFTGSTSVGSTLMGLAAQNIVKSSMELGGNAPLIVFDDADLERAVEGA 284

Query: 242 MAAKMRNMGEACTAANRFLVQESVAQEFTRKFAAAMGALSTGRGTDPASQVGPLINNGAR 301
           + AK+RN G++C AANR  VQ+ +A +F   F+  M  +  G        +GP+IN  A 
Sbjct: 285 ILAKLRNGGQSCVAANRIYVQDGIASDFVEAFSKRMSQMVLGHSIAEGVDLGPVINRDAV 344

Query: 302 DDIHALVTAAVDAGAVAVTGGAPVDGPGYFYQPTVLADVPNNAAILGQEIFGPVAPVTTF 361
           ++   LV  AV  GA   TGG   +G GYF++ TVL  VP +A I   EIFGP+A ++ F
Sbjct: 345 NNFQRLVDDAVTRGAELRTGGRAPEGAGYFFEATVLDRVPLDADIANTEIFGPIAAISRF 404

Query: 362 TTEQDAIKLANASEYGLAAYLYSRDFNRLLRVAEQIEFGMVGFNAGIISNAAAPFGGVKQ 421
           +T+++ I+ AN + +GLA Y+++ + +R L VA+Q+E G+VG N G+ SN AAPFGG+KQ
Sbjct: 405 STQEEVIQRANDTPFGLAGYVFTENLDRALNVADQLETGLVGINNGVPSNPAAPFGGMKQ 464

Query: 422 SGLGREGGSEGIAEYTTTQYIGIA 445
           SGLGREG  EG+ EY   +Y  IA
Sbjct: 465 SGLGREGSHEGLEEYQEIRYYNIA 488


Lambda     K      H
   0.317    0.131    0.376 

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: 512
Number of extensions: 16
Number of successful extensions: 1
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: 450
Length of database: 493
Length adjustment: 33
Effective length of query: 417
Effective length of database: 460
Effective search space:   191820
Effective search space used:   191820
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