GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gabD in Herbaspirillum seropedicae SmR1

Align succinate-semialdehyde dehydrogenase [NAD(P)+] (EC 1.2.1.16) (characterized)
to candidate HSERO_RS05645 HSERO_RS05645 succinate-semialdehyde dehdyrogenase

Query= BRENDA::Q0K2K1
         (483 letters)



>FitnessBrowser__HerbieS:HSERO_RS05645
          Length = 493

 Score =  538 bits (1386), Expect = e-157
 Identities = 269/486 (55%), Positives = 352/486 (72%), Gaps = 7/486 (1%)

Query: 1   MELQHTALLRSHCLIDGEWTGAQSGAELAVCNPATGERIGSVPLAGAAEAEQAVRAAERA 60
           + LQ   L+    LI  +W GA  G +L V +PATG+   SVP  GAA+A  AV AA  A
Sbjct: 4   LTLQRQDLMPGAQLIGADWRGAADGRQLDVSDPATGQVFASVPDGGAADARAAVEAAVAA 63

Query: 61  LPAWRAQTGKARAAVLRRWADLMLAHQEDLARLMTAEQGKPLPEARGEVAYAASFLEWFG 120
             AWRA   K RA +++RW DL+LAHQ+DL RL++ EQGKPL EA+GEVAYAAS++EWFG
Sbjct: 64  FAAWRATPAKQRAGIIKRWNDLLLAHQDDLGRLISREQGKPLAEAKGEVAYAASYVEWFG 123

Query: 121 EEAKRVDGEVLASPRSSQKMLVLREPVGVCAAITPWNFPAAMITRKVGPALAAGCTIIVK 180
           EEA R +G+++ +P + ++M+ L+EPVGV AAITPWNFPAAMI RK+ PALAAGCT++ K
Sbjct: 124 EEATRANGDIIPAPVTGRRMMALKEPVGVVAAITPWNFPAAMIARKIAPALAAGCTVVCK 183

Query: 181 PAEQTPLTALALAVLGEQAGVPRGVLQVVTGD---AVQIGGVLCASPVVRKLSFTGSTAI 237
           PAE TPLT+LAL  L ++AGVP GV+ +VT       ++  V  A   VRK+SFTGSTA+
Sbjct: 184 PAEDTPLTSLALVRLAQEAGVPVGVINIVTASRERTPEVVDVWLADGRVRKISFTGSTAV 243

Query: 238 GKLLMAQCAGTVKKLSLELGGNAPLIIFDDADLDRAVEGILASKFRNSGQTCVCANRIYV 297
           GK L    A T+KKLSLELGGNAP I+FDDAD+D A++G++A+KFRN GQTCV  NRIYV
Sbjct: 244 GKHLARHSADTLKKLSLELGGNAPFIVFDDADVDAAIDGVMAAKFRNGGQTCVSPNRIYV 303

Query: 298 HDRVYDEVARRLVSAVEQLRPGHGVDSGVTQGPLIDADAVAKVEAHIADALAQGATVLTG 357
            ++VYD    +L + V  L+ G   D     GP+I+A A+AK++ H+ DA+A+GA V+TG
Sbjct: 304 QEKVYDAFVDKLGARVAALKVGPATDPASQIGPMINARAIAKIDQHVRDAIARGARVITG 363

Query: 358 GQRHALGG----TFFAPTVLANATASMRVAREETFGPLAPLFRFTSEAEVVAMANDTESG 413
           G+R    G     ++APTVLA+ T +M+ + EETFGP+AP+ RF +E EV+A AN T  G
Sbjct: 364 GKRLQGPGFGSDNYYAPTVLADVTGAMQCSCEETFGPVAPITRFATEDEVIAAANATPFG 423

Query: 414 LAAYFFSRDMAKIWRVAQGLEYGMVGINTGLISNEVAPFGGVKQSGLGREGSRHGIDEYL 473
           LAAYF+S D+ +I RV   LE G+VG+N G ++ E APFGGVK+SG GREGS HG+D+YL
Sbjct: 424 LAAYFYSTDVRRIHRVTDALESGIVGVNEGALAAEAAPFGGVKESGYGREGSVHGLDDYL 483

Query: 474 ETKYLC 479
            TKY+C
Sbjct: 484 HTKYVC 489


Lambda     K      H
   0.319    0.133    0.390 

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: 691
Number of extensions: 24
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: 483
Length of database: 493
Length adjustment: 34
Effective length of query: 449
Effective length of database: 459
Effective search space:   206091
Effective search space used:   206091
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 52 (24.6 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