GapMind for catabolism of small carbon sources

 

Aligments for a candidate for iolA in Shewanella amazonensis SB2B

Align methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate 6938534 Sama_2637 succinate-semialdehyde dehydrogenase (NAD(P)(+)) (RefSeq)

Query= BRENDA::P42412
         (487 letters)



>lcl|FitnessBrowser__SB2B:6938534 Sama_2637 succinate-semialdehyde
           dehydrogenase (NAD(P)(+)) (RefSeq)
          Length = 480

 Score =  241 bits (614), Expect = 5e-68
 Identities = 149/473 (31%), Positives = 240/473 (50%), Gaps = 7/473 (1%)

Query: 6   KLKNYINGEWVESKTDQYEDVVNPATKEVLCQVPISTKEDIDYAAQTAAEAFKTWSKVAV 65
           K K YINGEW ++ + +   + NPAT E +  VP+  +++   A   A  A   W  +  
Sbjct: 10  KTKCYINGEWRDALSGETVTIANPATNEAIASVPVMGRDETREAIAAAEAALPAWRALTA 69

Query: 66  PRRARILFNFQQLLSQHKEELAHLITIENGKNTKEALGEVGRGIENVEFAAGAPSLMMGD 125
             R   L  + +L+ ++ ++LA ++T E GK   EA GEV      +E+ A     + GD
Sbjct: 70  KERGAKLRRWYELMLENADDLALMMTTEQGKPLAEAKGEVVYAASFIEWFAEEAKRLYGD 129

Query: 126 SLASIATDVEAANYRYPIGVVGGIAPFNFPMMVPCWMFPMAIALGNTFILKPSERTPLLT 185
           ++     D      +  +GV   I P+NFP  +       A+A G T I+KP+ +TP   
Sbjct: 130 TIPGHQGDKRIMVIKQGVGVTAAITPWNFPAAMITRKAGPALAAGCTMIVKPAPQTPFTA 189

Query: 186 EKLVELFEKAGLPKGVFNVVYG-AHDVVNGILEHPEIKAISFVGSKPVGEYVYKKGSENL 244
             L EL  +AG+P GVF+VV G A  + N + E+P ++ +SF GS  VG  + ++ +  L
Sbjct: 190 LALAELAAEAGIPPGVFSVVTGDAVAIGNELCENPVVRKLSFTGSTGVGIKLMQQCAPTL 249

Query: 245 KRVQSLTGAKNHTIVLNDANLEDTVTNIVGAAFGSAGERCMACAVVTVEEGIADEFMAKL 304
           K+V    G     IV NDA+L+  V   + + + +AG+ C+    + V++G+ D F  KL
Sbjct: 250 KKVSLELGGNAPFIVFNDADLDAAVEGAMISKYRNAGQTCVCANRLYVQDGVYDAFAQKL 309

Query: 305 QEKVADIKIGNGLDDGVFLGPVIREDNKKRTLSYIEKGLEEGARLVCDGRENVSDDGYFV 364
              VA +K+GNG + GV  GP+I     ++  S+++  L++GA LV  G+      G F+
Sbjct: 310 AAAVAKLKVGNGAEPGVTTGPLINAAALEKVQSHLQDALDKGATLVAGGKPL---GGNFM 366

Query: 365 GPTIFDNVTTEMTIWKDEIFAPVLSVIRVKNLKEAIEIANKSEFANGACLFTSNSNAIRY 424
            P I  NV   M + ++E F P+  + R  ++ + I  AN +EF   A  +  + + I  
Sbjct: 367 EPAIVTNVDASMKVAREETFGPLAPLFRFSDVDDVIRQANDTEFGLAAYFYGRDISLIWK 426

Query: 425 FRENIDAGMLGINLGVPAPMAFFPFSGWKSSFFGTLHANGKDSVDFYTRKKVV 477
             E ++ GM+G+N G+       PF G KSS  G      K  +D Y   K +
Sbjct: 427 VAEALEYGMVGVNTGL-ISTEVAPFGGMKSSGLG--REGSKYGIDEYVEIKYI 476


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: 570
Number of extensions: 26
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: 480
Length adjustment: 34
Effective length of query: 453
Effective length of database: 446
Effective search space:   202038
Effective search space used:   202038
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 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