GapMind for catabolism of small carbon sources

 

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

Align 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized)
to candidate Pf1N1B4_4355 Gamma-glutamyl-aminobutyraldehyde dehydrogenase (EC 1.2.1.-)

Query= BRENDA::P23883
         (495 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4355
          Length = 496

 Score =  546 bits (1407), Expect = e-160
 Identities = 278/489 (56%), Positives = 345/489 (70%), Gaps = 4/489 (0%)

Query: 9   WQDKALSLAIENRLFINGEYTAAAENETFETVDPVTQAPLAKIARGKSVDIDRAMSAARG 68
           W+ +  SL +E R FI+G+Y  A   +TFE + PV    LA IA     D + A+  AR 
Sbjct: 8   WEQRFQSLTLEGRAFIDGQYCPALSGDTFECISPVDGRFLANIASTDEADANAAVQVARR 67

Query: 69  VFERGDWSLSSPAKRKAVLNKLADLMEAHAEELALLETLDTGKPIRHSLRDDIPGAARAI 128
            FE G W+   PA+RK VL + ADL+  + EELALLETLD GKPI  S+  DIP  A AI
Sbjct: 68  TFESGIWAKLPPAERKRVLIRFADLILQNQEELALLETLDMGKPISDSMSIDIPATANAI 127

Query: 129 RWYAEAIDKVYGEVATTSSHELAMIVREPVGVIAAIVPWNFPLLLTCWKLGPALAAGNSV 188
           RW AEAIDK+Y EVA T   +L +I REP GV+AAIVPWNFPL++  WK  PALAAGNS 
Sbjct: 128 RWSAEAIDKIYDEVAATPHDQLGLITREPAGVVAAIVPWNFPLIMASWKFAPALAAGNSF 187

Query: 189 ILKPSEKSPLSAIRLAGLAKEAGLPDGVLNVVTGFGHEAGQALSRHNDIDAIAFTGSTRT 248
           ILKPSEKSPL+AIR+A LA EAG+P GV NV+ GFGH  G+AL+ H D+D +AFTGST  
Sbjct: 188 ILKPSEKSPLTAIRIAQLALEAGIPKGVFNVLPGFGHTVGKALALHMDVDVLAFTGSTAI 247

Query: 249 GKQLLKDAGDSNMKRVWLEAGGKSANIVFADCPDLQQAASATAAGIFYNQGQVCIAGTRL 308
            KQLL  AG SNMKRVWLEAGGKS N+VFAD PDL+ AA A  + I +NQG+VC AG+RL
Sbjct: 248 AKQLLIYAGQSNMKRVWLEAGGKSPNVVFADAPDLRAAARAAVSAIAFNQGEVCTAGSRL 307

Query: 309 LLEESIADEFLALLKQQAQNWQPGHPLDPATTMGTLIDCAHADSVHSFIREGESKGQLLL 368
           L+E SI ++F+ LL +  Q W+PGH LDP TT+G ++D    D+V  +I+ G+ +G  L+
Sbjct: 308 LVERSIREQFIPLLVEALQAWKPGHALDPETTVGAVVDQRQLDNVLRYIQVGKDQGAQLI 367

Query: 369 DGRNAGLAAAIG----PTIFVDVDPNASLSREEIFGPVLVVTRFTSEEQALQLANDSQYG 424
            G N  LA   G    P IF  V    +++REEIFGPVL +  F + E+ALQ+ANDS +G
Sbjct: 368 AGGNRTLADTGGLYVEPAIFDGVTNAMTIAREEIFGPVLSLITFDTAEEALQIANDSIFG 427

Query: 425 LGAAVWTRDLSRAHRMSRRLKAGSVFVNNYNDGDMTVPFGGYKQSGNGRDKSLHALEKFT 484
           L A VWT +LS+AH  +R L+AGSV+VN Y+ GDMT PFGG+KQSGNGRDKSLHA +K+T
Sbjct: 428 LAAGVWTSNLSKAHTFARGLRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKSLHAFDKYT 487

Query: 485 ELKTIWISL 493
           ELK  WI L
Sbjct: 488 ELKATWIKL 496


Lambda     K      H
   0.317    0.133    0.389 

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: 629
Number of extensions: 14
Number of successful extensions: 2
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: 495
Length of database: 496
Length adjustment: 34
Effective length of query: 461
Effective length of database: 462
Effective search space:   212982
Effective search space used:   212982
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