GapMind for catabolism of small carbon sources

 

Alignments for a candidate for iolA in Pseudomonas stutzeri RCH2

Align methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate GFF4164 Psest_4237 succinate-semialdehyde dehydrogenase

Query= BRENDA::P42412
         (487 letters)



>FitnessBrowser__psRCH2:GFF4164
          Length = 482

 Score =  251 bits (641), Expect = 4e-71
 Identities = 148/450 (32%), Positives = 238/450 (52%), Gaps = 3/450 (0%)

Query: 10  YINGEWVESKTDQYEDVVNPATKEVLCQVPISTKEDIDYAAQTAAEAFKTWSKVAVPRRA 69
           YI+G W+++ + Q   V NPAT E L  VP     +   A   A  A   W  +    R+
Sbjct: 14  YIDGAWLDADSGQTISVNNPATGETLGTVPKMGAAETRRAIDAAERALPAWRDLTAKERS 73

Query: 70  RILFNFQQLLSQHKEELAHLITIENGKNTKEALGEVGRGIENVEFAAGAPSLMMGDSLAS 129
           + L  + +LL +++++L  L+T+E GK   EA GE+      +E+ A     + GD++  
Sbjct: 74  QKLRRWFELLMENQDDLGRLMTLEQGKPLAEAKGEIAYAASFIEWFAEEAKRIYGDTIPG 133

Query: 130 IATDVEAANYRYPIGVVGGIAPFNFPMMVPCWMFPMAIALGNTFILKPSERTPLLTEKLV 189
              D      + PIGV   I P+NFP  +       A+A G T ++KP+ +TP     +V
Sbjct: 134 HQKDKRIIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVIKPASQTPFSALAMV 193

Query: 190 ELFEKAGLPKGVFNVVYG-AHDVVNGILEHPEIKAISFVGSKPVGEYVYKKGSENLKRVQ 248
           EL E+AG+PKGV +VV G A D+ N +  +P+++ ISF GS  VG  + ++ +  +K+V 
Sbjct: 194 ELAERAGIPKGVLSVVTGSAGDIGNELTANPKVRKISFTGSTEVGAKLMEQCAPGIKKVS 253

Query: 249 SLTGAKNHTIVLNDANLEDTVTNIVGAAFGSAGERCMACAVVTVEEGIADEFMAKLQEKV 308
              G     IV +DA+L++ V   V + + +AG+ C+    + V++G+ D F  K Q  V
Sbjct: 254 LELGGNAPFIVFDDADLDEAVKGAVQSKYRNAGQTCVCVNRIYVQDGVYDTFAEKFQAAV 313

Query: 309 ADIKIGNGLDDGVFLGPVIREDNKKRTLSYIEKGLEEGARLVCDGRENVSDDGYFVGPTI 368
           A +++GNGL++G  LGP+I +    +   +IE  + +GARLV  G+ +     YF  PT+
Sbjct: 314 AKLRVGNGLEEGTDLGPLIDDRAAAKVREHIEDAVAQGARLVAGGQAHALGGSYF-EPTV 372

Query: 369 FDNVTTEMTIWKDEIFAPVLSVIRVKNLKEAIEIANKSEFANGACLFTSNSNAIRYFREN 428
             NV     + K+E F P+  + R K+  +AI  AN +EF   +  +  +   +    E 
Sbjct: 373 LVNVPDSAKVAKEETFGPLAPLFRFKDEADAIAKANDTEFGLASYFYARDLGRVFRVAEA 432

Query: 429 IDAGMLGINLGVPAPMAFFPFSGWKSSFFG 458
           ++ GM+GIN G+       PF G KSS  G
Sbjct: 433 LEYGMVGINTGL-ISTEVAPFGGVKSSGLG 461


Lambda     K      H
   0.318    0.136    0.396 

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: 527
Number of extensions: 19
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: 487
Length of database: 482
Length adjustment: 34
Effective length of query: 453
Effective length of database: 448
Effective search space:   202944
Effective search space used:   202944
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