GapMind for catabolism of small carbon sources

 

Alignments for a candidate for astD in Herbaspirillum seropedicae SmR1

Align N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized)
to candidate HSERO_RS05645 HSERO_RS05645 succinate-semialdehyde dehdyrogenase

Query= curated2:B0T8I8
         (484 letters)



>FitnessBrowser__HerbieS:HSERO_RS05645
          Length = 493

 Score =  219 bits (558), Expect = 2e-61
 Identities = 166/474 (35%), Positives = 225/474 (47%), Gaps = 21/474 (4%)

Query: 1   MSGGLFIDGVWRAGA-GAQATSVDPTTGEVIWRQATASTAEVAAAVEAARKAFPAWADRS 59
           M G   I   WR  A G Q    DP TG+V         A+  AAVEAA  AF AW    
Sbjct: 12  MPGAQLIGADWRGAADGRQLDVSDPATGQVFASVPDGGAADARAAVEAAVAAFAAWRATP 71

Query: 60  REERIAVLRRYKDVLVARTGTFAEALSRETGKALWETKAELGSMAGKVEASIKAYDERTG 119
            ++R  +++R+ D+L+A        +SRE GK L E K E+   A  VE   +      G
Sbjct: 72  AKQRAGIIKRWNDLLLAHQDDLGRLISREQGKPLAEAKGEVAYAASYVEWFGEEATRANG 131

Query: 120 EHANDMAFGRAVLRHRAH-GVMAVLGPFNFPGHLPNGHIVPALLAGDTVVFKPSEETPLA 178
           +       GR ++  +   GV+A + P+NFP  +    I PAL AG TVV KP+E+TPL 
Sbjct: 132 DIIPAPVTGRRMMALKEPVGVVAAITPWNFPAAMIARKIAPALAAGCTVVCKPAEDTPLT 191

Query: 179 GQLLVEALEEAGVPAGVINLVQGGRE-----VGQALIDQEIDGLLFTGSAAAGAFFRRHF 233
              LV   +EAGVP GVIN+V   RE     V   L D  +  + FTGS A G    RH 
Sbjct: 192 SLALVRLAQEAGVPVGVINIVTASRERTPEVVDVWLADGRVRKISFTGSTAVGKHLARHS 251

Query: 234 ADRPDVILALELGGNNPLVVWDAGDPEAVAALIVQSAFITTGQRCSCARRLIVSDDAAGR 293
           AD     L+LELGGN P +V+D  D +A    ++ + F   GQ C    R+ V +     
Sbjct: 252 ADTLKK-LSLELGGNAPFIVFDDADVDAAIDGVMAAKFRNGGQTCVSPNRIYVQEKVYD- 309

Query: 294 AVIDAVAALSERLVIGPWNGGQEPFMGPLISDRAAAM-------ALA-GAKAMPGQTLRA 345
           A +D + A    L +GP        +GP+I+ RA A        A+A GA+ + G   R 
Sbjct: 310 AFVDKLGARVAALKVGPATDPASQ-IGPMINARAIAKIDQHVRDAIARGARVITGGK-RL 367

Query: 346 MTSVDGLSRAFVSPGLVDVTGE-TVPDEELFAPLLQVRRVGSFEEAIAAANATRYGLSAG 404
                G    +    L DVTG      EE F P+  + R  + +E IAAANAT +GL+A 
Sbjct: 368 QGPGFGSDNYYAPTVLADVTGAMQCSCEETFGPVAPITRFATEDEVIAAANATPFGLAAY 427

Query: 405 LVSNETAHWDRFLTRIRAGVVNWNRPTTGAAGTMPFGGLGNSGNHRPSAYYAAD 458
             S +     R    + +G+V  N     AA   PFGG+  SG  R  + +  D
Sbjct: 428 FYSTDVRRIHRVTDALESGIVGVNEGAL-AAEAAPFGGVKESGYGREGSVHGLD 480


Lambda     K      H
   0.318    0.134    0.395 

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: 582
Number of extensions: 25
Number of successful extensions: 5
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: 484
Length of database: 493
Length adjustment: 34
Effective length of query: 450
Effective length of database: 459
Effective search space:   206550
Effective search space used:   206550
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