GapMind for catabolism of small carbon sources

 

Aligments for a candidate for dopDH in Burkholderia phytofirmans PsJN

Align Alpha-ketoglutaric semialdehyde dehydrogenase 1; alphaKGSA dehydrogenase 1; 2,5-dioxovalerate dehydrogenase 1; 2-oxoglutarate semialdehyde dehydrogenase 1; KGSADH-I; Succinate-semialdehyde dehydrogenase [NAD(+)]; SSDH; EC 1.2.1.26; EC 1.2.1.24 (characterized)
to candidate BPHYT_RS22430 BPHYT_RS22430 succinate-semialdehyde dehydrogenase

Query= SwissProt::Q1JUP4
         (481 letters)



>lcl|FitnessBrowser__BFirm:BPHYT_RS22430 BPHYT_RS22430
           succinate-semialdehyde dehydrogenase
          Length = 486

 Score =  369 bits (948), Expect = e-106
 Identities = 206/483 (42%), Positives = 276/483 (57%), Gaps = 5/483 (1%)

Query: 1   MANVTYTDTQLL-----IDGEWVDAASGKTIDVVNPATGKPIGRVAHAGIADLDRALAAA 55
           M  ++  D  LL     I GEW  A  G T +V NPATG+ I  V   G A+  RA+  A
Sbjct: 1   MTTLSLKDPSLLKSHAYIAGEWQGADDGTTFEVKNPATGETIATVPRMGTAETRRAIDTA 60

Query: 56  QSGFEAWRKVPAHERAATMRKAAALVRERADAIAQLMTQEQGKPLTEARVEVLSAADIIE 115
            + + AWR   A +RA  +RK   L+ E AD +A+++T EQGKPL EA+ E+  AA  +E
Sbjct: 61  NAAWPAWRATTAKQRAVILRKWHDLMMENADDLAKILTTEQGKPLAEAKGEIQYAASFLE 120

Query: 116 WFADEGRRVYGRIVPPRNLGAQQTVVKEPVGPVAAFTPWNFPVNQVVRKLSAALATGCSF 175
           WFA+EG+RV G  +P      +  V KEP+G  AA TPWNFP   + RK+  ALA GC  
Sbjct: 121 WFAEEGKRVNGDTIPTPASDKRIVVTKEPIGVCAAITPWNFPAAMITRKVGPALAAGCPI 180

Query: 176 LVKAPEETPASPAALLRAFVDAGVPAGVIGLVYGDPAEISSYLIPHPVIRKVTFTGSTPV 235
           +VK  E TP S  AL      AGVP GV  +V G+P  I + +  +P++RK++FTGSTPV
Sbjct: 181 IVKPAEATPLSALALAVLAERAGVPRGVFNVVTGEPKAIGAEMTGNPIVRKLSFTGSTPV 240

Query: 236 GKQLASLAGLHMKRATMELGGHAPVIVAEDADVALAVKAAGGAKFRNAGQVCISPTRFLV 295
           G+ L +     +K+ ++ELGG+AP IV +DAD+  AV  A  +K+RN+GQ C+   RF V
Sbjct: 241 GRLLMAQCAPTVKKVSLELGGNAPFIVFDDADLDAAVAGAIASKYRNSGQTCVCTNRFYV 300

Query: 296 HNSIRDEFTRALVKHAEGLKVGNGLEEGTTLGALANPRRLTAMASVIDNARKVGASIETG 355
           H+ + D F   L    E LKVG G E+G T G L N   +  + S I++A   GA I TG
Sbjct: 301 HDKVYDAFAEKLRVAVEQLKVGRGTEDGVTQGPLINDAAVLKVESHIEDALAKGARIVTG 360

Query: 356 GERIGSEGNFFAPTVIANVPLDADVFNNEPFGPVAAIRGFDKLEEAIAEANRLPFGLAGY 415
           G+R      FF PTV+A+V     V  +E FGP+A +  F   EE I  AN   FGLA Y
Sbjct: 361 GKRHALGHGFFEPTVLADVTPAMKVARDETFGPLAPLFRFSSDEEVIRLANDTEFGLASY 420

Query: 416 AFTRSFANVHLLTQRLEVGMLWINQPATPWPEMPFGGVKDSGYGSEGGPEALEPYLVTKS 475
            ++R    V  + + LE GM+ IN         PFGGVK SG G EG    ++ Y+V K 
Sbjct: 421 FYSRDIGRVWRVAEALEYGMVGINTGLISNEVAPFGGVKQSGLGREGSHYGIDDYVVIKY 480

Query: 476 VTV 478
           + V
Sbjct: 481 LCV 483


Lambda     K      H
   0.318    0.134    0.393 

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: 633
Number of extensions: 26
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: 481
Length of database: 486
Length adjustment: 34
Effective length of query: 447
Effective length of database: 452
Effective search space:   202044
Effective search space used:   202044
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 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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