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_RS05645 HSERO_RS05645 succinate-semialdehyde dehdyrogenase

Query= SwissProt::Q1JUP4
         (481 letters)



>FitnessBrowser__HerbieS:HSERO_RS05645
          Length = 493

 Score =  355 bits (912), Expect = e-102
 Identities = 195/472 (41%), Positives = 269/472 (56%), Gaps = 7/472 (1%)

Query: 12  LIDGEWVDAASGKTIDVVNPATGKPIGRVAHAGIADLDRALAAAQSGFEAWRKVPAHERA 71
           LI  +W  AA G+ +DV +PATG+    V   G AD   A+ AA + F AWR  PA +RA
Sbjct: 17  LIGADWRGAADGRQLDVSDPATGQVFASVPDGGAADARAAVEAAVAAFAAWRATPAKQRA 76

Query: 72  ATMRKAAALVRERADAIAQLMTQEQGKPLTEARVEVLSAADIIEWFADEGRRVYGRIVPP 131
             +++   L+    D + +L+++EQGKPL EA+ EV  AA  +EWF +E  R  G I+P 
Sbjct: 77  GIIKRWNDLLLAHQDDLGRLISREQGKPLAEAKGEVAYAASYVEWFGEEATRANGDIIPA 136

Query: 132 RNLGAQQTVVKEPVGPVAAFTPWNFPVNQVVRKLSAALATGCSFLVKAPEETPASPAALL 191
              G +   +KEPVG VAA TPWNFP   + RK++ ALA GC+ + K  E+TP +  AL+
Sbjct: 137 PVTGRRMMALKEPVGVVAAITPWNFPAAMIARKIAPALAAGCTVVCKPAEDTPLTSLALV 196

Query: 192 RAFVDAGVPAGVIGLVYGD---PAEISSYLIPHPVIRKVTFTGSTPVGKQLASLAGLHMK 248
           R   +AGVP GVI +V        E+    +    +RK++FTGST VGK LA  +   +K
Sbjct: 197 RLAQEAGVPVGVINIVTASRERTPEVVDVWLADGRVRKISFTGSTAVGKHLARHSADTLK 256

Query: 249 RATMELGGHAPVIVAEDADVALAVKAAGGAKFRNAGQVCISPTRFLVHNSIRDEFTRALV 308
           + ++ELGG+AP IV +DADV  A+     AKFRN GQ C+SP R  V   + D F   L 
Sbjct: 257 KLSLELGGNAPFIVFDDADVDAAIDGVMAAKFRNGGQTCVSPNRIYVQEKVYDAFVDKLG 316

Query: 309 KHAEGLKVGNGLEEGTTLGALANPRRLTAMASVIDNARKVGASIETGGERIGSEG----N 364
                LKVG   +  + +G + N R +  +   + +A   GA + TGG+R+   G    N
Sbjct: 317 ARVAALKVGPATDPASQIGPMINARAIAKIDQHVRDAIARGARVITGGKRLQGPGFGSDN 376

Query: 365 FFAPTVIANVPLDADVFNNEPFGPVAAIRGFDKLEEAIAEANRLPFGLAGYAFTRSFANV 424
           ++APTV+A+V         E FGPVA I  F   +E IA AN  PFGLA Y ++     +
Sbjct: 377 YYAPTVLADVTGAMQCSCEETFGPVAPITRFATEDEVIAAANATPFGLAAYFYSTDVRRI 436

Query: 425 HLLTQRLEVGMLWINQPATPWPEMPFGGVKDSGYGSEGGPEALEPYLVTKSV 476
           H +T  LE G++ +N+ A      PFGGVK+SGYG EG    L+ YL TK V
Sbjct: 437 HRVTDALESGIVGVNEGALAAEAAPFGGVKESGYGREGSVHGLDDYLHTKYV 488


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: 705
Number of extensions: 32
Number of successful extensions: 3
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: 493
Length adjustment: 34
Effective length of query: 447
Effective length of database: 459
Effective search space:   205173
Effective search space used:   205173
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