GapMind for catabolism of small carbon sources

 

Alignments for a candidate for astD in Pseudomonas fluorescens FW300-N2C3

Align Succinylglutamic semialdehyde dehydrogenase (EC 1.2.1.71) (characterized)
to candidate AO356_26740 AO356_26740 succinate-semialdehyde dehydrogenase

Query= reanno::pseudo13_GW456_L13:PfGW456L13_1974
         (488 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_26740
          Length = 485

 Score =  208 bits (529), Expect = 4e-58
 Identities = 157/461 (34%), Positives = 226/461 (49%), Gaps = 9/461 (1%)

Query: 5   YIAGEWLAGGGEA-FESLNPVTQQVLWSGVGATAGQVESAVQAARQAFPDWARRTLEERI 63
           YI G+W+     A  + +NP T +VL         +   AV+AA +A+P W  R   ER 
Sbjct: 17  YIDGQWVGADNAATVDVINPATGEVLARVPAIQGSETRRAVEAADRAWPAWRARPAAERA 76

Query: 64  SVLEAFAAALKNHADELAHTIGEETGKPLWEAATEVTSMVNKIAISVQSYRERTGEK-SG 122
           ++L+ +  A+ ++ D+LA  +  E GKPL EA  E+    + +    +  R   GE    
Sbjct: 77  ALLDRWYQAMIDNLDDLALILTCEQGKPLAEAQGEIRYGASFVKWFAEEARRVYGETIQA 136

Query: 123 PLGDATAVLRHKPHGVVAVFGPYNFPGHLPNGHIVPALLAGNSVLFKPSELTPKVAELTV 182
           P GD   +   +P GV A   P+NFP  +      PAL AG +++ KPS+LTP  A    
Sbjct: 137 PSGDRRLLTLKQPVGVCAAITPWNFPNAMITRKCAPALAAGCTIVVKPSDLTPLSALALA 196

Query: 183 KCWIEAGLPAGVLNLLQG-ARETGIALAANPGIDGLFFTGSSRTGNHLHQQFAGRPDKIL 241
                 G+PAGV N++ G     G  L  NP +  L FTGS+  G  L +Q A    K L
Sbjct: 197 VLAERVGIPAGVFNVVTGMPAGIGEELTGNPTVRKLSFTGSTAVGRLLMRQSA-EHIKRL 255

Query: 242 ALEMGGNNPLVVDQVADLDAAVYTIIQSAFISAGQRCTCARRLLVPQGAWGDSLLARLVA 301
           +LE+GGN P +V   ADL+ AV  I+ S F +AGQ C CA R+LV  G + +    RLV 
Sbjct: 256 SLELGGNAPFIVFDDADLEQAVTGIMLSKFRNAGQTCVCANRILVQDGIY-ERFAQRLVE 314

Query: 302 VSSTLSVGAFDQQPAPFMGSVVSLGAAKALMDAQEHLLANGAVALLEMTQPQAQSALLTP 361
               L VG         +G +++  A   +    +  L+ GA  LL    P+  S  + P
Sbjct: 315 EVGKLKVGD-GLDAGVNIGPLINTAAVSKVARHIDEALSQGA-RLLCGEIPKGDSQFVQP 372

Query: 362 GIL-DVSAVADRPDEELFGPLLQVIRYADFEAAIAEANDTAYGLAAGLLSDSEARYQQFW 420
            +L +  A     +EE FGP+  ++R++  E A+A AN T YGLAA   +    R  +F 
Sbjct: 373 TVLGEAHAGMLLANEETFGPVAPLMRFSTEEEALASANATPYGLAAYFFTQDLRRSWRFG 432

Query: 421 LESRAGIVNWNKQLTGAASSAPFGGVGASGNHRASAYYAAD 461
                G+V  N  L  +   APFGG+  SG  R  + Y  D
Sbjct: 433 EALEFGMVGLNTGLI-SMDVAPFGGIKQSGLGREGSKYGLD 472


Lambda     K      H
   0.316    0.132    0.388 

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: 551
Number of extensions: 30
Number of successful extensions: 6
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: 488
Length of database: 485
Length adjustment: 34
Effective length of query: 454
Effective length of database: 451
Effective search space:   204754
Effective search space used:   204754
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