GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__HerbieS:HSERO_RS05645 HSERO_RS05645
           succinate-semialdehyde dehdyrogenase
          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 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