GapMind for catabolism of small carbon sources

 

Alignments for a candidate for astD in Pseudomonas fluorescens FW300-N1B4

Align N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized)
to candidate Pf1N1B4_4355 Gamma-glutamyl-aminobutyraldehyde dehydrogenase (EC 1.2.1.-)

Query= curated2:Q2SXN9
         (487 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4355
          Length = 496

 Score =  196 bits (498), Expect = 2e-54
 Identities = 152/470 (32%), Positives = 234/470 (49%), Gaps = 20/470 (4%)

Query: 5   FIDGAWVDG-AGPVFASRNPGTNERVWEGASASADDVERAVASARRAFAA--WSALDLDA 61
           FIDG +    +G  F   +P     +   AS    D   AV  ARR F +  W+ L    
Sbjct: 22  FIDGQYCPALSGDTFECISPVDGRFLANIASTDEADANAAVQVARRTFESGIWAKLPPAE 81

Query: 62  RCTIVKRFAALLVERKEALATMIGRETGKPLWEART-EVASMAAKVDISITAYHERTGEK 120
           R  ++ RFA L+++ +E LA +   + GKP+ ++ + ++ + A  +  S  A  +   E 
Sbjct: 82  RKRVLIRFADLILQNQEELALLETLDMGKPISDSMSIDIPATANAIRWSAEAIDKIYDEV 141

Query: 121 RAPMADGVAVLRHRPHGVVAVFGPYNFPGHLPNGHIVPALIAGNTVVFKPSELAPGVARA 180
            A   D + ++   P GVVA   P+NFP  + +    PAL AGN+ + KPSE +P  A  
Sbjct: 142 AATPHDQLGLITREPAGVVAAIVPWNFPLIMASWKFAPALAAGNSFILKPSEKSPLTAIR 201

Query: 181 TVEIWRDAGLPAGVLNLVQGEKDT-GVALANHRQIDGLFFTGSSDTGTLLHKQFGGRPEI 239
             ++  +AG+P GV N++ G   T G ALA H  +D L FTGS+     L    G     
Sbjct: 202 IAQLALEAGIPKGVFNVLPGFGHTVGKALALHMDVDVLAFTGSTAIAKQLLIYAGQSNMK 261

Query: 240 VLALEMGGNNPLVV-AEVEDIDAAVHHAIQSAFLSAGQRCTCARRILVPRGAFGDRFVAR 298
            + LE GG +P VV A+  D+ AA   A+ +   + G+ CT   R+LV R +  ++F+  
Sbjct: 262 RVWLEAGGKSPNVVFADAPDLRAAARAAVSAIAFNQGEVCTAGSRLLVER-SIREQFIPL 320

Query: 299 LADVASKITASVFDADPQPFMGAVISARAASRLVAAQARLVGLG---ASPIIEMKQR--- 352
           L + A +        DP+  +GAV+  R    ++    R + +G    + +I    R   
Sbjct: 321 LVE-ALQAWKPGHALDPETTVGAVVDQRQLDNVL----RYIQVGKDQGAQLIAGGNRTLA 375

Query: 353 DPALGFVNAAILD-VTNVRELPDEEHFGPLAQIVRYTDLDDAIARANDTAFGLSAGLLAD 411
           D    +V  AI D VTN   +  EE FGP+  ++ +   ++A+  AND+ FGL+AG+   
Sbjct: 376 DTGGLYVEPAIFDGVTNAMTIAREEIFGPVLSLITFDTAEEALQIANDSIFGLAAGVWTS 435

Query: 412 DEQAWHTFRRAIRAGIVNWNRPTNGASSAAPFGGAGRSGNHRPSAYYAAD 461
           +    HTF R +RAG V W    +G    APFGG  +SGN R  + +A D
Sbjct: 436 NLSKAHTFARGLRAGSV-WVNQYDGGDMTAPFGGFKQSGNGRDKSLHAFD 484


Lambda     K      H
   0.320    0.134    0.402 

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: 535
Number of extensions: 31
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: 487
Length of database: 496
Length adjustment: 34
Effective length of query: 453
Effective length of database: 462
Effective search space:   209286
Effective search space used:   209286
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 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