GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gabD in Nocardioides daejeonensis MJ31

Align Succinate-semialdehyde dehydrogenase; SsaDH; EC 1.2.1.16 (characterized)
to candidate WP_110207112.1 DNK54_RS11350 NAD-dependent succinate-semialdehyde dehydrogenase

Query= SwissProt::Q8GAI8
         (450 letters)



>NCBI__GCF_003194585.1:WP_110207112.1
          Length = 461

 Score =  449 bits (1156), Expect = e-131
 Identities = 239/444 (53%), Positives = 298/444 (67%), Gaps = 3/444 (0%)

Query: 2   LATLASATSEDAVAALEAACAAQTSWARTAPRVRAEILRRAFDLVTARSEDFALLMTLEM 61
           + T+  +   DAVAA++AA AA  +WA T  R R E LRR FDL+   +E    L+  E 
Sbjct: 17  IETVPDSNVLDAVAAVDAAAAAFPAWAATPARTRGETLRRCFDLMLRDAELLVGLIAGEN 76

Query: 62  GKPLAEARGEVAYGAEFLRWFSEETVRDYGRYLTTPEGKNKILVQHKPVGPCLLITPWNF 121
           GK LA+AR EV Y AEF RWFSEE VR  G Y   P GK K LV   PVG   L+TPWNF
Sbjct: 77  GKSLADARAEVNYAAEFFRWFSEEAVRSEGTYGDAPAGKAKTLVTRAPVGVAALVTPWNF 136

Query: 122 PLAMATRKVAPAVAAGCTMVLKPAKLTPLTSQLFAQTMMEAGLPAGVLNVVSSSSASGIS 181
           P AMATRK+APA+AAGCT+VLKPA  TPLT+   A+ M EAG+P GV+NVV ++ A+ + 
Sbjct: 137 PAAMATRKIAPALAAGCTVVLKPAAETPLTALALAEIMREAGVPDGVVNVVPTTDAAAVV 196

Query: 182 GPLLKDSRLRKVSFTGSTPVGKRLMSDASRHVLRTSMELGGNAPFVVFEDADLDKAVEGA 241
              L+D R+RK+SFTGST VG+ L+  A+  VL  SMELGGNAPFV+  DAD+D AV GA
Sbjct: 197 TAWLEDPRIRKISFTGSTGVGRALLRQAADRVLNASMELGGNAPFVITADADVDAAVAGA 256

Query: 242 MAAKMRNMGEACTAANRFLVQESVAQEFTRKFAAAMGALSTGRGTDPASQVGPLINNGAR 301
           M AK R  G+ACTAANRF V   +A EF  KF  A+ AL  G   D  +QVGP+I+  A 
Sbjct: 257 MIAKFRGGGQACTAANRFYVHRDIAAEFVEKFGDAVAALRVGPAADETNQVGPVISEKAL 316

Query: 302 DDIHALVTAAVDAGA-VAVTGGAPVDGPGYFYQPTVLADVPNNAAILGQEIFGPVAPVTT 360
             +  LV AAV  GA +AV G  P    G+F+ PT+L DVP  A IL +EIFGPVAP+ T
Sbjct: 317 GTLTTLVDAAVADGARIAVQGTVP--EKGWFFPPTILVDVPVGAPILSEEIFGPVAPIVT 374

Query: 361 FTTEQDAIKLANASEYGLAAYLYSRDFNRLLRVAEQIEFGMVGFNAGIISNAAAPFGGVK 420
           +T E + ++  N +E+GLAAY+Y+      LR+ EQI+ GMVG N GI+S+ AAPFGGVK
Sbjct: 375 WTDEAEMLESVNDTEFGLAAYVYAGRLQDALRLGEQIDAGMVGINRGIVSDPAAPFGGVK 434

Query: 421 QSGLGREGGSEGIAEYTTTQYIGI 444
           QSG+GREG  EG+ EY  T+Y  +
Sbjct: 435 QSGIGREGAHEGMREYQETRYYSV 458


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: 544
Number of extensions: 23
Number of successful extensions: 2
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: 461
Length adjustment: 33
Effective length of query: 417
Effective length of database: 428
Effective search space:   178476
Effective search space used:   178476
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