GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aldA in Herbaspirillum seropedicae SmR1

Align lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized)
to candidate HSERO_RS05645 HSERO_RS05645 succinate-semialdehyde dehdyrogenase

Query= BRENDA::P25553
         (479 letters)



>FitnessBrowser__HerbieS:HSERO_RS05645
          Length = 493

 Score =  313 bits (803), Expect = 6e-90
 Identities = 176/468 (37%), Positives = 264/468 (56%), Gaps = 11/468 (2%)

Query: 18  WRGDA---WIDVVNPATEAVISRIPDGQAEDARKAIDAAERAQPEWEALPAIERASWLRK 74
           WRG A    +DV +PAT  V + +PDG A DAR A++AA  A   W A PA +RA  +++
Sbjct: 22  WRGAADGRQLDVSDPATGQVFASVPDGGAADARAAVEAAVAAFAAWRATPAKQRAGIIKR 81

Query: 75  ISAGIRERASEISALIVEEGGKIQQLAEVEVAFTADYIDYMAEWARRYEGEIIQSDRPGE 134
            +  +     ++  LI  E GK    A+ EVA+ A Y+++  E A R  G+II +   G 
Sbjct: 82  WNDLLLAHQDDLGRLISREQGKPLAEAKGEVAYAASYVEWFGEEATRANGDIIPAPVTGR 141

Query: 135 NILLFKRALGVTTGILPWNFPFFLIARKMAPALLTGNTIVIKPSEFTPNNAIAFAKIVDE 194
            ++  K  +GV   I PWNFP  +IARK+APAL  G T+V KP+E TP  ++A  ++  E
Sbjct: 142 RMMALKEPVGVVAAITPWNFPAAMIARKIAPALAAGCTVVCKPAEDTPLTSLALVRLAQE 201

Query: 195 IGLPRGVFNLVLGRGETVGQEL---AGNPKVAMVSMTGSVSAGEKIMATAAKNITKVCLE 251
            G+P GV N+V    E   + +     + +V  +S TGS + G+ +   +A  + K+ LE
Sbjct: 202 AGVPVGVINIVTASRERTPEVVDVWLADGRVRKISFTGSTAVGKHLARHSADTLKKLSLE 261

Query: 252 LGGKAPAIVMDDADLELAVKAIVDSRVINSGQVCNCAERVYVQKGIYDQFVNRLGEAMQA 311
           LGG AP IV DDAD++ A+  ++ ++  N GQ C    R+YVQ+ +YD FV++LG  + A
Sbjct: 262 LGGNAPFIVFDDADVDAAIDGVMAAKFRNGGQTCVSPNRIYVQEKVYDAFVDKLGARVAA 321

Query: 312 VQFGNPAERNDIAMGPLINAAALERVEQKVARAVEEGARVAFGGKAVEGKGY----YYPP 367
           ++ G PA      +GP+INA A+ +++Q V  A+  GARV  GGK ++G G+    YY P
Sbjct: 322 LKVG-PATDPASQIGPMINARAIAKIDQHVRDAIARGARVITGGKRLQGPGFGSDNYYAP 380

Query: 368 TLLLDVRQEMSIMHEETFGPVLPVVAFDTLEDAISMANDSDYGLTSSIYTQNLNVAMKAI 427
           T+L DV   M    EETFGPV P+  F T ++ I+ AN + +GL +  Y+ ++    +  
Sbjct: 381 TVLADVTGAMQCSCEETFGPVAPITRFATEDEVIAAANATPFGLAAYFYSTDVRRIHRVT 440

Query: 428 KGLKFGETYINRENFEAMQGFHAGWRKSGIGGADGKHGLHEYLQTQVV 475
             L+ G   +N     A      G ++SG G     HGL +YL T+ V
Sbjct: 441 DALESGIVGVNEGALAAEAAPFGGVKESGYGREGSVHGLDDYLHTKYV 488


Lambda     K      H
   0.318    0.135    0.392 

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: 554
Number of extensions: 30
Number of successful extensions: 4
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: 479
Length of database: 493
Length adjustment: 34
Effective length of query: 445
Effective length of database: 459
Effective search space:   204255
Effective search space used:   204255
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