GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__BFirm:BPHYT_RS22430
          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:

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