GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dopDH in Herbaspirillum seropedicae SmR1

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 HSERO_RS19695 HSERO_RS19695 aldehyde dehydrogenase

Query= SwissProt::Q1JUP4
         (481 letters)



>FitnessBrowser__HerbieS:HSERO_RS19695
          Length = 480

 Score =  449 bits (1154), Expect = e-130
 Identities = 225/472 (47%), Positives = 313/472 (66%)

Query: 6   YTDTQLLIDGEWVDAASGKTIDVVNPATGKPIGRVAHAGIADLDRALAAAQSGFEAWRKV 65
           Y D QL IDG +      +  +V +PATG  +GR+  A  AD++ A+ AA   F+ WR+V
Sbjct: 2   YPDLQLYIDGRFHGVEGRRYQEVRDPATGDVLGRLPWAERADIEEAIQAAHRAFQQWRQV 61

Query: 66  PAHERAATMRKAAALVRERADAIAQLMTQEQGKPLTEARVEVLSAADIIEWFADEGRRVY 125
              ER+  +R+AAAL RERA A+A  +T + GKPL +A  E+++AA+ ++W A+EGRR+Y
Sbjct: 62  SPLERSDILRRAAALARERAQAMAPAITMDNGKPLADAVAEIINAAEHLDWHAEEGRRLY 121

Query: 126 GRIVPPRNLGAQQTVVKEPVGPVAAFTPWNFPVNQVVRKLSAALATGCSFLVKAPEETPA 185
           GR+V  R+   +Q VV+EPVG  AA +PWNFP  Q ++K++AA+A GC+ ++K P E+PA
Sbjct: 122 GRVVGARHPEVRQLVVREPVGVCAAISPWNFPFGQAMKKVAAAMAAGCTVVLKGPSESPA 181

Query: 186 SPAALLRAFVDAGVPAGVIGLVYGDPAEISSYLIPHPVIRKVTFTGSTPVGKQLASLAGL 245
           +   + + F DAGVPAGV  +V G  +EIS +LI  P++R ++FTGS PVG +LA+ A L
Sbjct: 182 AIVLMAQLFHDAGVPAGVFNIVSGVSSEISQHLIESPLVRNISFTGSVPVGSKLAAQAAL 241

Query: 246 HMKRATMELGGHAPVIVAEDADVALAVKAAGGAKFRNAGQVCISPTRFLVHNSIRDEFTR 305
           HMKR +MELGGHAPV+V +DA+V  A +     K RNAGQVC+SP+RF V   I   F  
Sbjct: 242 HMKRMSMELGGHAPVLVFDDAEVEPAARLLARLKTRNAGQVCVSPSRFYVQKGIYARFVT 301

Query: 306 ALVKHAEGLKVGNGLEEGTTLGALANPRRLTAMASVIDNARKVGASIETGGERIGSEGNF 365
           A  +    +KVG G E G  +G L + RR  A+  +ID+A   G+ + TGG R+G  G+F
Sbjct: 302 AFAEALLQIKVGPGHEPGVQMGPLIHGRRFEAVQGLIDDALAQGSELVTGGARLGQRGHF 361

Query: 366 FAPTVIANVPLDADVFNNEPFGPVAAIRGFDKLEEAIAEANRLPFGLAGYAFTRSFANVH 425
           +APT+I  VP  A V   EPFGP+AA+  F + EEAIA AN LP GLA Y FT+S    H
Sbjct: 362 YAPTLITGVPPSARVMQEEPFGPIAAVTPFSQAEEAIAMANALPLGLASYVFTQSLDTAH 421

Query: 426 LLTQRLEVGMLWINQPATPWPEMPFGGVKDSGYGSEGGPEALEPYLVTKSVT 477
            +++ L+ GM+ IN      PE+PFGG+ +SG+GSEGG E  E +LVTK ++
Sbjct: 422 RVSRDLQAGMVNINHSGMAHPELPFGGIGESGFGSEGGVEGFESFLVTKMIS 473


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: 688
Number of extensions: 31
Number of successful extensions: 2
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: 480
Length adjustment: 34
Effective length of query: 447
Effective length of database: 446
Effective search space:   199362
Effective search space used:   199362
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 (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