GapMind for catabolism of small carbon sources

 

Aligments for a candidate for dopDH in Klebsiella michiganensis M5al

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 BWI76_RS15205 BWI76_RS15205 succinate-semialdehyde dehydrogenase

Query= SwissProt::Q1JUP4
         (481 letters)



>lcl|FitnessBrowser__Koxy:BWI76_RS15205 BWI76_RS15205
           succinate-semialdehyde dehydrogenase
          Length = 461

 Score =  271 bits (694), Expect = 3e-77
 Identities = 161/441 (36%), Positives = 232/441 (52%), Gaps = 18/441 (4%)

Query: 29  VNPATGKPIGRVAHAGIADLDRALAAAQSGFEAWRKVPAHERAATMRKAAALVRERADAI 88
           VNP TG+ +  +  A    +D A+A A+ G+  WRKV   +RA T+R   A +R R++A+
Sbjct: 11  VNPTTGETLSSLPWASEQQVDSAIALAEQGYRQWRKVSVAQRATTLRNVGAAMRARSEAL 70

Query: 89  AQLMTQEQGKPLTEARVEVLSAADIIEWFADEGRRVYGRIVPPRNLGAQQTVVKE----- 143
           AQ+++ E GKP+ +AR EV  +A++ +W+A+ G         P  L  + T+V++     
Sbjct: 71  AQMISLEMGKPIAQARGEVAKSANLCDWYAEHG---------PAMLNTEATLVEDNKAVI 121

Query: 144 ---PVGPVAAFTPWNFPVNQVVRKLSAALATGCSFLVKAPEETPASPAALLRAFVDAGVP 200
              P+G + A  PWNFPV QV+R     L  G S+L+K       S A +   F  AGVP
Sbjct: 122 EYRPMGAILAIMPWNFPVWQVLRGAVPILLAGNSYLLKHAPNVLGSAAMIGEIFAAAGVP 181

Query: 201 AGVIGLVYGDPAEISSYLIPHPVIRKVTFTGSTPVGKQLASLAGLHMKRATMELGGHAPV 260
            GV G V      +S  +I  P I  VT TGS   GK + + AG  +K+  +ELGG  P 
Sbjct: 182 EGVFGWVNATNDGVSQ-MINDPRIAAVTVTGSVRAGKAIGAQAGAALKKCVLELGGSDPF 240

Query: 261 IVAEDADVALAVKAAGGAKFRNAGQVCISPTRFLVHNSIRDEFTRALVKHAEGLKVGNGL 320
           IV  DAD+  AVKAA   +++N GQVC +  RF+V   I + FT+  V     LK+G+  
Sbjct: 241 IVLNDADLDEAVKAAVIGRYQNTGQVCAAAKRFIVEAGIAEAFTQKFVAAVAALKMGDPR 300

Query: 321 EEGTTLGALANPRRLTAMASVIDNARKVGASIETGGERIGSEGNFFAPTVIANVPLDADV 380
           +E   +G +A       +   +    K GA++  G E+I   GN++APTV+ NV  +   
Sbjct: 301 DEQNYIGPMARFDLRDELHEQVRATLKEGATLLLGAEKIEGAGNYYAPTVLGNVTAEMTG 360

Query: 381 FNNEPFGPVAAIRGFDKLEEAIAEANRLPFGLAGYAFTRSFANVHLLTQRLEVGMLWINQ 440
           F  E FGPVA I      + A+A AN   FGL+   +T S          LE G ++IN 
Sbjct: 361 FREELFGPVATITEARDADHALALANESEFGLSATVYTTSETQARRFADELECGGVFING 420

Query: 441 PATPWPEMPFGGVKDSGYGSE 461
                  + FGGVK SG+G E
Sbjct: 421 YCASDARVAFGGVKKSGFGRE 441


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: 503
Number of extensions: 30
Number of successful extensions: 4
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: 461
Length adjustment: 33
Effective length of query: 448
Effective length of database: 428
Effective search space:   191744
Effective search space used:   191744
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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 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