GapMind for catabolism of small carbon sources

 

Aligments for a candidate for davD in Herbaspirillum seropedicae SmR1

Align glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized)
to candidate HSERO_RS05645 HSERO_RS05645 succinate-semialdehyde dehdyrogenase

Query= BRENDA::Q88RC0
         (480 letters)



>lcl|FitnessBrowser__HerbieS:HSERO_RS05645 HSERO_RS05645
           succinate-semialdehyde dehdyrogenase
          Length = 493

 Score =  527 bits (1358), Expect = e-154
 Identities = 254/472 (53%), Positives = 343/472 (72%), Gaps = 9/472 (1%)

Query: 15  INGEWLDADNGQTIKVTNPATGEVIGTVPKMGTAETRRAIEAADKALPAWRALTAKERSA 74
           I  +W  A +G+ + V++PATG+V  +VP  G A+ R A+EAA  A  AWRA  AK+R+ 
Sbjct: 18  IGADWRGAADGRQLDVSDPATGQVFASVPDGGAADARAAVEAAVAAFAAWRATPAKQRAG 77

Query: 75  KLRRWFELMIENQDDLARLMTTEQGKPLAEAKGEIAYAASFIEWFAEEAKRIYGDTIPGH 134
            ++RW +L++ +QDDL RL++ EQGKPLAEAKGE+AYAAS++EWF EEA R  GD IP  
Sbjct: 78  IIKRWNDLLLAHQDDLGRLISREQGKPLAEAKGEVAYAASYVEWFGEEATRANGDIIPAP 137

Query: 135 QPDKRLIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVLKPASQTPYSALALVE 194
              +R++ +K+P+GV AAITPWNFPAAMI RK  PALAAGCT+V KPA  TP ++LALV 
Sbjct: 138 VTGRRMMALKEPVGVVAAITPWNFPAAMIARKIAPALAAGCTVVCKPAEDTPLTSLALVR 197

Query: 195 LAHRAGIPAGVLSVVTGS---AGEVGGELTGNSLVRKLSFTGSTEIGRQLMEECAKDIKK 251
           LA  AG+P GV+++VT S     EV      +  VRK+SFTGST +G+ L    A  +KK
Sbjct: 198 LAQEAGVPVGVINIVTASRERTPEVVDVWLADGRVRKISFTGSTAVGKHLARHSADTLKK 257

Query: 252 VSLELGGNAPFIVFDDADLDKAVEGAIISKYRNNGQTCVCANRIYVQDGVYDAFAEKLAA 311
           +SLELGGNAPFIVFDDAD+D A++G + +K+RN GQTCV  NRIYVQ+ VYDAF +KL A
Sbjct: 258 LSLELGGNAPFIVFDDADVDAAIDGVMAAKFRNGGQTCVSPNRIYVQEKVYDAFVDKLGA 317

Query: 312 AVAKLKIGNGLEEGTTTGPLIDGKAVAKVQEHIEDAVSKGAKVLSGGKLIEG------NF 365
            VA LK+G   +  +  GP+I+ +A+AK+ +H+ DA+++GA+V++GGK ++G      N+
Sbjct: 318 RVAALKVGPATDPASQIGPMINARAIAKIDQHVRDAIARGARVITGGKRLQGPGFGSDNY 377

Query: 366 FEPTILVDVPKTAAVAKEETFGPLAPLFRFKDEAEVIAMSNDTEFGLASYFYARDMSRVF 425
           + PT+L DV      + EETFGP+AP+ RF  E EVIA +N T FGLA+YFY+ D+ R+ 
Sbjct: 378 YAPTVLADVTGAMQCSCEETFGPVAPITRFATEDEVIAAANATPFGLAAYFYSTDVRRIH 437

Query: 426 RVAEALEYGMVGINTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIKYLC 477
           RV +ALE G+VG+N G ++ E APFGG+K SG GREGS +G++DYL  KY+C
Sbjct: 438 RVTDALESGIVGVNEGALAAEAAPFGGVKESGYGREGSVHGLDDYLHTKYVC 489


Lambda     K      H
   0.317    0.134    0.384 

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: 660
Number of extensions: 34
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: 480
Length of database: 493
Length adjustment: 34
Effective length of query: 446
Effective length of database: 459
Effective search space:   204714
Effective search space used:   204714
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 (21.6 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint 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