GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gabD in Williamsia sterculiae CPCC 203464

Align Succinate-semialdehyde dehydrogenase; SsaDH; EC 1.2.1.16 (characterized)
to candidate WP_076476004.1 BW971_RS02050 NAD-dependent succinate-semialdehyde dehydrogenase

Query= SwissProt::Q8GAI8
         (450 letters)



>NCBI__GCF_900156495.1:WP_076476004.1
          Length = 500

 Score =  496 bits (1276), Expect = e-145
 Identities = 256/448 (57%), Positives = 324/448 (72%), Gaps = 5/448 (1%)

Query: 2   LATLASATSEDAVAALEAACAAQTSWARTAPRVRAEILRRAFDLVTARSEDFALLMTLEM 61
           L  +A A  +DA+ AL+ + AA   WA T+PR R+ ILR AFDL+T R+ D ALLMTLEM
Sbjct: 51  LTQVADAGPDDAMLALKQSVAAADDWAATSPRERSVILRAAFDLITERAADLALLMTLEM 110

Query: 62  GKPLAEARGEVAYGAEFLRWFSEETVRDYGRYLTTPEGKNKILVQHKPVGPCLLITPWNF 121
           GK L +++ E+AYGAEFLRWFSEE VR  GRY  +P G  +ILV H+PVGPCL ITPWNF
Sbjct: 111 GKALPDSKSEIAYGAEFLRWFSEEAVRINGRYTQSPGGTGRILVTHQPVGPCLAITPWNF 170

Query: 122 PLAMATRKVAPAVAAGCTMVLKPAKLTPLTSQLFAQTMMEAGLPAGVLNVVSSSSASGIS 181
           PLAM TRK+ PA+AAG T+++KPA  TPLT    A+   EAGLP GVL V+ +S AS + 
Sbjct: 171 PLAMGTRKIGPALAAGNTIIVKPAAETPLTMLALAKIFAEAGLPPGVLAVLPTSDASAVC 230

Query: 182 GPLLKDSRLRKVSFTGSTPVGKRLMSDASRHVLRTSMELGGNAPFVVFEDADLDKAVEGA 241
            PL++D+R+RK++FTGST VG+ L+  A+ +V RTSMELGGNAPF+VF+DADLD A++GA
Sbjct: 231 TPLIEDTRIRKITFTGSTGVGRILLGQAAANVQRTSMELGGNAPFIVFDDADLDAALDGA 290

Query: 242 MAAKMRNMGEACTAANRFLVQESVAQEFTRKFAAAMGALSTGRGTDPASQVGPLINNGAR 301
            AAKMRN GEACTAANRFLV +SVA+EFT    A M AL+ G G    + +GPLI+   R
Sbjct: 291 FAAKMRNGGEACTAANRFLVHDSVAEEFTDGLIARMQALTVGPGYADGTTLGPLISEKQR 350

Query: 302 DDIHALVTAAVDAGAVAVTGGAPV-----DGPGYFYQPTVLADVPNNAAILGQEIFGPVA 356
           + +   VT AV  GA    GG         G G+FY PTVL +VP  A I   EIFGPVA
Sbjct: 351 NSVAQKVTDAVADGARVRLGGEQARAEQHGGDGWFYPPTVLDEVPVGAEITRGEIFGPVA 410

Query: 357 PVTTFTTEQDAIKLANASEYGLAAYLYSRDFNRLLRVAEQIEFGMVGFNAGIISNAAAPF 416
            ++TF T  +AI  AN +EYGLAAY+Y+RD +R L V+++++ G+VG N G+IS+ AAPF
Sbjct: 411 VISTFGTVDEAIAAANDTEYGLAAYIYTRDLDRALSVSDRLQTGLVGVNRGVISDVAAPF 470

Query: 417 GGVKQSGLGREGGSEGIAEYTTTQYIGI 444
           GG KQSGLGREGG EGI E+ TT+Y+ +
Sbjct: 471 GGEKQSGLGREGGLEGIGEFLTTKYVAL 498


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: 565
Number of extensions: 19
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: 500
Length adjustment: 33
Effective length of query: 417
Effective length of database: 467
Effective search space:   194739
Effective search space used:   194739
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