GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__HerbieS:HSERO_RS05645
          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:

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