GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gabD in Phaeobacter inhibens BS107

Align Succinate-semialdehyde dehydrogenase; SsaDH; EC 1.2.1.16 (characterized)
to candidate GFF2285 PGA1_c23170 succinate-semialdehyde dehdyrogenase GabD

Query= SwissProt::Q8GAI8
         (450 letters)



>FitnessBrowser__Phaeo:GFF2285
          Length = 474

 Score =  481 bits (1237), Expect = e-140
 Identities = 241/442 (54%), Positives = 311/442 (70%)

Query: 1   MLATLASATSEDAVAALEAACAAQTSWARTAPRVRAEILRRAFDLVTARSEDFALLMTLE 60
           +LA++ASA   DA AAL+AA AA   WA   PR R+E+LR+A++L+T R + FA L+TLE
Sbjct: 29  VLASVASADIADADAALDAAEAAMKDWAARTPRQRSEVLRKAWELMTKRLDYFANLITLE 88

Query: 61  MGKPLAEARGEVAYGAEFLRWFSEETVRDYGRYLTTPEGKNKILVQHKPVGPCLLITPWN 120
            GK   +A+GE  Y AEF RWF+EE VR  G     P    +I+VQHKP G  +L+TPWN
Sbjct: 89  NGKAGTDAKGEATYAAEFFRWFAEEAVRADGMITHAPASGARIVVQHKPAGLAVLVTPWN 148

Query: 121 FPLAMATRKVAPAVAAGCTMVLKPAKLTPLTSQLFAQTMMEAGLPAGVLNVVSSSSASGI 180
           +P AM TRK+APA+AAGC +++KPA  TPLT       + EAG+PAG++NV+ S     +
Sbjct: 149 YPAAMGTRKIAPALAAGCGVIIKPASETPLTMLALMPLLEEAGVPAGLVNVLPSRKTGSL 208

Query: 181 SGPLLKDSRLRKVSFTGSTPVGKRLMSDASRHVLRTSMELGGNAPFVVFEDADLDKAVEG 240
              +L D R+R VSFTGST VG++L+  A+  VL+ +MELGGNAP VVFEDAD+D A+EG
Sbjct: 209 VDHMLHDPRIRVVSFTGSTGVGRKLLKGAADQVLKPAMELGGNAPVVVFEDADMDVAIEG 268

Query: 241 AMAAKMRNMGEACTAANRFLVQESVAQEFTRKFAAAMGALSTGRGTDPASQVGPLINNGA 300
            M AKMRN+GEACTAANR  V E +A EFT++ +AAM AL  G GTDP+  VGPL+N   
Sbjct: 269 TMLAKMRNLGEACTAANRIYVHEDIADEFTKRLSAAMSALKVGDGTDPSVDVGPLVNADT 328

Query: 301 RDDIHALVTAAVDAGAVAVTGGAPVDGPGYFYQPTVLADVPNNAAILGQEIFGPVAPVTT 360
           RD + A V  AV  GA    GG   +G G++Y PTVL++V  +A  +  EIFGPVA + T
Sbjct: 329 RDKVAAFVADAVAKGAKVECGGTTPNGKGFYYPPTVLSNVSEDAECVRDEIFGPVAAIQT 388

Query: 361 FTTEQDAIKLANASEYGLAAYLYSRDFNRLLRVAEQIEFGMVGFNAGIISNAAAPFGGVK 420
           FT + + I  AN +EYGL AY++S DF R L+V EQ+E+GMVG N G++S+ AAPFGGVK
Sbjct: 389 FTNQDEVIARANDTEYGLVAYVFSEDFKRALQVCEQLEYGMVGLNRGLVSDPAAPFGGVK 448

Query: 421 QSGLGREGGSEGIAEYTTTQYI 442
           QSGLGREGG EG+ E+  TQYI
Sbjct: 449 QSGLGREGGHEGMLEFMETQYI 470


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: 537
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: 474
Length adjustment: 33
Effective length of query: 417
Effective length of database: 441
Effective search space:   183897
Effective search space used:   183897
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 17 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