GapMind for catabolism of small carbon sources

 

Aligments for a candidate for dopDH in Paraburkholderia bryophila 376MFSha3.1

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 H281DRAFT_03540 H281DRAFT_03540 succinate semialdehyde dehydrogenase (EC 1.2.1.16)

Query= SwissProt::Q1JUP4
         (481 letters)



>lcl|FitnessBrowser__Burk376:H281DRAFT_03540 H281DRAFT_03540
           succinate semialdehyde dehydrogenase (EC 1.2.1.16)
          Length = 479

 Score =  372 bits (955), Expect = e-107
 Identities = 204/462 (44%), Positives = 273/462 (59%), Gaps = 2/462 (0%)

Query: 13  IDGEWVDAASGKTIDVVNPATGKPIGRVAHAGIADLDRALAAAQSGFEAWRKVPAHERAA 72
           I GEW + AS  T  V+NPATG+ I +VA  G  +  +A+AAA+  F AWR + A ER+A
Sbjct: 11  IGGEWYEGAS--TYPVLNPATGEVIAQVAKGGAVEATQAIAAAERAFPAWRSLTAKERSA 68

Query: 73  TMRKAAALVRERADAIAQLMTQEQGKPLTEARVEVLSAADIIEWFADEGRRVYGRIVPPR 132
            +++   L+ E  DA+A L+T+EQGKPL EAR EV  AA   EWFA+E +R YG ++P  
Sbjct: 69  RVKRWGELMLEHRDALAALLTREQGKPLAEARGEVGYAASFFEWFAEEAKRAYGDVIPSP 128

Query: 133 NLGAQQTVVKEPVGPVAAFTPWNFPVNQVVRKLSAALATGCSFLVKAPEETPASPAALLR 192
           N  A+  V +EPVG VAA TPWNFP+  + RK   ALA GC+ ++K  EETP S  AL  
Sbjct: 129 NPNAKIIVTREPVGVVAAITPWNFPLAMITRKAGPALAAGCTMVLKPSEETPLSALALAV 188

Query: 193 AFVDAGVPAGVIGLVYGDPAEISSYLIPHPVIRKVTFTGSTPVGKQLASLAGLHMKRATM 252
               AG+P GV  +V GD   I   L    V+RK++FTGST VGK LA  +   +K+ ++
Sbjct: 189 LAEKAGIPPGVFNVVSGDAVAIGGALTESDVVRKLSFTGSTRVGKLLAKQSADTLKKLSL 248

Query: 253 ELGGHAPVIVAEDADVALAVKAAGGAKFRNAGQVCISPTRFLVHNSIRDEFTRALVKHAE 312
           ELGG+AP IV +DAD+  AV+ A  +KFRN GQ C+   RF V + I D FT AL + A 
Sbjct: 249 ELGGNAPFIVFDDADLDAAVQGAMASKFRNTGQTCVCVNRFYVQDGIYDAFTLALAQAAR 308

Query: 313 GLKVGNGLEEGTTLGALANPRRLTAMASVIDNARKVGASIETGGERIGSEGNFFAPTVIA 372
            ++VGN L+     G L N   LT + + + +A + GA + TG +     G F+ PTV+ 
Sbjct: 309 KMRVGNALQGDVEQGPLINQAALTKVEAHVADALQKGAKVLTGAKPHALGGTFYEPTVLV 368

Query: 373 NVPLDADVFNNEPFGPVAAIRGFDKLEEAIAEANRLPFGLAGYAFTRSFANVHLLTQRLE 432
           +      +   E FGPVAA   F   +EA+A AN  PFGL+ Y +TR  A    + + LE
Sbjct: 369 DASSSMLIAQEETFGPVAACFRFKTEDEAVAAANATPFGLSAYFYTRDLARAWRVGEALE 428

Query: 433 VGMLWINQPATPWPEMPFGGVKDSGYGSEGGPEALEPYLVTK 474
            GM+ IN+        PFGGVK SG G EG    L+ Y   K
Sbjct: 429 SGMVGINEGILSTEVAPFGGVKQSGLGREGSKYGLDEYTELK 470


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: 608
Number of extensions: 29
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: 479
Length adjustment: 34
Effective length of query: 447
Effective length of database: 445
Effective search space:   198915
Effective search space used:   198915
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.

Links

Downloads

Related tools

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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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, 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